diff --git a/aphylogeo/bin/FastTree b/aphylogeo/bin/FastTree deleted file mode 100755 index 301b59a1..00000000 Binary files a/aphylogeo/bin/FastTree and /dev/null differ diff --git a/aphylogeo/bin/FastTree.exe b/aphylogeo/bin/FastTree.exe deleted file mode 100644 index a0c083f3..00000000 Binary files a/aphylogeo/bin/FastTree.exe and /dev/null differ diff --git a/aphylogeo/bin/clustalw2 b/aphylogeo/bin/clustalw2 deleted file mode 100755 index 43d5e4f1..00000000 Binary files a/aphylogeo/bin/clustalw2 and /dev/null differ diff --git a/aphylogeo/bin/clustalw2.exe b/aphylogeo/bin/clustalw2.exe deleted file mode 100644 index 170d3c58..00000000 Binary files a/aphylogeo/bin/clustalw2.exe and /dev/null differ diff --git a/aphylogeo/bin/mafft-linux64/mafft.bat b/aphylogeo/bin/mafft-linux64/mafft.bat deleted file mode 100755 index 35fb1c1a..00000000 --- a/aphylogeo/bin/mafft-linux64/mafft.bat +++ /dev/null @@ -1,8 +0,0 @@ -#! /bin/bash -# sh -> bash for debian. By J. R. Peterson. 2015/Jun. - -pushd "`dirname "$0"`" > /dev/null 2>&1; rootdir="$PWD"; popd > /dev/null 2>&1; -MAFFT_BINARIES="$rootdir/mafftdir/libexec"; export MAFFT_BINARIES; - -"$rootdir/mafftdir/bin/mafft" "$@" -# input file name can have space diff --git a/aphylogeo/bin/mafft-linux64/mafftdir/bin/mafft b/aphylogeo/bin/mafft-linux64/mafftdir/bin/mafft deleted file mode 100755 index c5b1737d..00000000 --- a/aphylogeo/bin/mafft-linux64/mafftdir/bin/mafft +++ /dev/null @@ -1,3063 +0,0 @@ -#! /bin/bash -er=0; -myself=`dirname "$0"`/`basename "$0"`; export myself -version="v7.520 (2023/Mar/22)"; export version -LANG=C; export LANG -os=`uname` -progname=`basename "$0"` -windows="no" -if [ `echo $os | grep -i cygwin` ]; then - os="cygwin" - windows="yes" -elif [ `echo $os | grep -i msys` ]; then - os="msys" - windows="yes" -elif [ `echo $os | grep -i mingw` ]; then - os="mingw" - windows="yes" -elif [ `echo $os | grep -i darwin` ]; then - os="darwin" -elif [ `echo $os | grep -i sunos` ]; then - os="sunos" -elif [ `echo $os | grep -i linux` ]; then - os="linux" -else - os="unix" -fi -#export os # iranai -if [ "$windows" = "yes" ]; then - echo "" 1>&2 - echo "It may take a while before the calculation starts" 1>&2 - echo "if being scanned by anti-virus software." 1>&2 - echo "Also consider using a faster version for Windows 10:" 1>&2 - echo "https://mafft.cbrc.jp/alignment/software/wsl.html" 1>&2 -fi - -if [ "$MAFFT_BINARIES" ]; then - prefix="$MAFFT_BINARIES" -else - prefix=/usr/libexec/mafft -fi -export prefix # iranai - -if [ $# -gt 0 ]; then - if [ "$1" = "--man" ]; then - man "$prefix/mafft.1" - exit 0; - fi -fi - -if [ -x "$prefix/version" ]; then -# versionbin=`"$prefix/version" | awk '{print $1}'` # for cygwin - versionbin=`"$prefix/version"` # for cygwin 2.7 - else - versionbin="0.000" -fi - -if ! expr "$version" : v"$versionbin" > /dev/null ; then - echo "" 1>&2 - echo "v$versionbin != $version" 1>&2 - echo "" 1>&2 - echo "There is a problem in the configuration of your shell." 1>&2 - echo "Check the MAFFT_BINARIES environmental variable by" 1>&2 - echo "$ echo \$MAFFT_BINARIES" 1>&2 - echo "" 1>&2 - echo "This variable must be *unset*, unless you have installed MAFFT" 1>&2 - echo "with a special configuration. To unset this variable, type" 1>&2 - echo "$ unset MAFFT_BINARIES" 1>&2 - echo "or" 1>&2 - echo "% unsetenv MAFFT_BINARIES" 1>&2 - echo "Then retry" 1>&2 - echo "$ mafft input > output" 1>&2 - echo "" 1>&2 - echo "To keep this change permanently, edit setting files" 1>&2 - echo "(.bash_profile, .profile, .cshrc, etc) in your home directory" 1>&2 - echo "to delete the MAFFT_BINARIES line." 1>&2 - echo "On MacOSX, also edit or remove the .MacOSX/environment.plist file" 1>&2 - echo "and then re-login (MacOSX 10.6) or reboot (MacOSX 10.7)." 1>&2 - echo "" 1>&2 - echo "Please send a problem report to katoh@ifrec.osaka-u.ac.jp," 1>&2 - echo "if this problem remains." 1>&2 - echo "" 1>&2 - exit 1 - er=1 -fi - -defaultiterate=0 -defaultcycle=2 -defaultgop="1.53" -#defaultaof="0.123" -defaultaof="0.000" -defaultlaof="0.100" -defaultlgop="-2.00" -defaultfft=1 -defaultrough=0 -defaultdistance="ktuples" -#defaultdistance="local" -defaultweighti="2.7" -defaultweightr="0.0" -defaultweightm="1.0" -defaultdafs=0 -defaultmccaskill=0 -defaultcontrafold=0 -defaultalgopt=" " -defaultalgoptit=" " -defaultsbstmodel=" -b 62 " -defaultfmodel=" " -defaultkappa=" " -if [ $progname = "xinsi" -o $progname = "mafft-xinsi" ]; then - defaultfft=1 - defaultcycle=1 - defaultiterate=1000 - defaultdistance="scarna" - defaultweighti="3.2" - defaultweightr="8.0" - defaultweightm="2.0" - defaultmccaskill=1 - defaultcontrafold=0 - defaultdafs=0 - defaultalgopt=" -A " - defaultalgoptit=" -AB " ## chui - defaultaof="0.0" - defaultsbstmodel=" -b 62 " - defaultkappa=" " - defaultfmodel=" " # 2013/06/18 -elif [ $progname = "qinsi" -o $progname = "mafft-qinsi" ]; then - defaultfft=1 - defaultcycle=1 - defaultiterate=1000 - defaultdistance="global" - defaultweighti="3.2" - defaultweightr="8.0" - defaultweightm="2.0" - defaultmccaskill=1 - defaultcontrafold=0 - defaultdafs=0 - defaultalgopt=" -A " - defaultalgoptit=" -AB " ## chui - defaultaof="0.0" - defaultsbstmodel=" -b 62 " - defaultkappa=" " - defaultfmodel=" " # 2013/06/18 -elif [ $progname = "linsi" -o $progname = "mafft-linsi" ]; then - defaultfft=0 - defaultcycle=1 - defaultiterate=1000 - defaultdistance="local" -elif [ $progname = "ginsi" -o $progname = "mafft-ginsi" ]; then - defaultfft=1 - defaultcycle=1 - defaultiterate=1000 - defaultdistance="global" -elif [ $progname = "einsi" -o $progname = "mafft-einsi" ]; then - defaultfft=0 - defaultcycle=1 - defaultiterate=1000 - defaultdistance="localgenaf" -elif [ $progname = "fftns" -o $progname = "mafft-fftns" ]; then - defaultfft=1 - defaultcycle=2 - defaultdistance="ktuples" -elif [ $progname = "fftnsi" -o $progname = "mafft-fftnsi" ]; then - defaultfft=1 - defaultcycle=2 - defaultiterate=2 - defaultdistance="ktuples" -elif [ $progname = "nwns" -o $progname = "mafft-nwns" ]; then - defaultfft=0 - defaultcycle=2 - defaultdistance="ktuples" -elif [ $progname = "nwnsi" -o $progname = "mafft-nwnsi" ]; then - defaultfft=0 - defaultcycle=2 - defaultiterate=2 - defaultdistance="ktuples" -fi -outputfile="" -namelength=-1 -linelength=60 # Will change to -1 in the future -anysymbol=0 -parallelizationstrategy="BAATARI2" -kappa=$defaultkappa -sbstmodel=$defaultsbstmodel -fmodel=$defaultfmodel -nmodel=" " -gexp=0 -gop=$defaultgop -gopdist=$defaultgop -aof=$defaultaof -cycle=$defaultcycle -iterate=$defaultiterate -fft=$defaultfft -rough=$defaultrough -distance=$defaultdistance -forcefft=0 -memopt=" " -weightopt=" " -GGOP="-6.00" -LGOP="-6.00" -LEXP="-0.000" -GEXP="-0.000" -lgop=$defaultlgop -lexp="-0.100" -laof=$defaultlaof -pggop="-2.00" -pgexp="-0.10" -pgaof="0.10" -rgop="-1.530" -rgep="-0.000" -seqtype=" " -weighti=$defaultweighti -weightr=$defaultweightr -weightm=$defaultweightm -rnaalifold=0 -dafs=$defaultdafs -mccaskill=$defaultmccaskill -contrafold=$defaultcontrafold -progressfile="/dev/stderr" -anchorfile="/dev/null" -anchoropt="" -#maxanchorseparation=1000 -maxanchorseparation=-1 # 2023/Jan/11 -debug=0 -sw=0 -algopt=$defaultalgopt -algoptit=$defaultalgoptit -#algspecified=0 -pairspecified=0 -scorecalcopt=" " -coreout=0 -corethr="0.5" -corewin="100" -coreext=" " -outputformat="pir" -f2clext="-N" -outorder="input" -seed="x" -seedtable="x" -auto=0 -groupsize=-1 -partsize=50 -partdist="ktuples" -partorderopt=" -x " -treeout=0 -nodeout=0 -distout=0 -treein=0 -topin=0 -treeinopt=" " -seedfiles="/dev/null" -seedtablefile="/dev/null" -pdblist="/dev/null" -ownlist="/dev/null" -strdir="$PWD" -scorematrix="/dev/null" -textmatrix="/dev/null" -treeinfile="/dev/null" -codonposfile="/dev/null" -codonscorefile="/dev/null" -rnascoremtx=" " -laraparams="/dev/null" -foldalignopt=" " -treealg=" -X 0.1 " -sueff="1.0" -maxambiguous="1.0" -dofilter=0 -scoreoutarg=" " -numthreads=0 -numthreadsit=-1 -numthreadstb=-1 -randomseed=0 -addfile="/dev/null" -addarg0=" " -addarg=" " -addsinglearg=" " -add2ndhalfarg=" " -mapoutfile="/dev/null" -fragment=0 -legacygapopt=" " -mergetable="/dev/null" -mergearg=" " -seedoffset=0 -outnum=" " -last_e=5000 -last_m=3 -last_subopt=" " -last_once=" " -adjustdirection=0 -tuplesize=6 -termgapopt=" -O " -#termgapopt=" " # gap/gap ga kakenai node -similarityoffset="0.0" -unalignlevel="0.0" -unalignspecified=0 -spfactor="100.0" -shiftpenaltyspecified=0 -opdistspecified=0 -allowshift=0 -enrich=0 # ato de kezuru -enrichseq=0 # ato de kezuru -enrichstr=0 # ato de kezuru -seektarget="" # ato de kezuru -dashserver="https://sysimm.org/dash/REST1.0/" -newdash=0 -newdash_originalsequenceonly=0 -exclude_ho=0 -fixthreshold="0.0" -bunkatsuopt=" " -npickup=0 -minimumweight="0.00001" # 2016/Mar -usenaivepairscore=" " -oldgenafparam=0 -sprigorous=0 -treeext="none" -initialramusage="20GB" -focusarg=" " -lhlimit=" " -mpiscript="/dev/null" -if [ $# -gt 0 ]; then - if [ "$1" = "--version" ]; then - echo "$version" 1>&2 - exit 0; - elif [ "$1" = "--help" -o "$1" = "--info" ]; then - shift - er=1; - fi - while [ $# -gt 1 ]; - do - if [ "$1" = "--auto" ]; then - auto=1 - elif [ "$1" = "--anysymbol" ]; then - anysymbol=1 - elif [ "$1" = "--preservecase" ]; then - anysymbol=1 - elif [ "$1" = "--clustalout" ]; then - outputformat="clustal" - elif [ "$1" = "--phylipout" ]; then - outputformat="phylip" - elif [ "$1" = "--reorder" ]; then - outorder="aligned" - partorderopt=" " - elif [ "$1" = "--inputorder" ]; then - outorder="input" - partorderopt=" -x " - elif [ "$1" = "--unweight" ]; then - weightopt=" -u " - elif [ "$1" = "--termgappenalty" ]; then - termgapopt=" " - elif [ "$1" = "--alga" ]; then - algopt=" " - algoptit=" " -# algspecified=1 - elif [ "$1" = "--algq" ]; then - algopt=" -Q " - algoptit=" " - echo "" 1>&2 - echo "--algq is no longer supported!" 1>&2 - echo "" 1>&2 - exit 1; -# algspecified=1 - elif [ "$1" = "--linelength" ]; then - shift - linelength=`expr "$1" - 0` - if [ $linelength -eq 0 ]; then - echo "Line length = 0 ?" 1>&2 - exit - fi - elif [ "$1" = "--namelength" ]; then - shift - namelength=`expr "$1" - 0` - if ! expr "$1" : "[0-9]" > /dev/null ; then - echo "Specify the length of name in clustal format output!" 1>&2 - exit - fi - elif [ "$1" = "--groupsize" ]; then - shift - groupsize=`expr "$1" - 0` - if ! expr "$1" : "[0-9]" > /dev/null ; then - echo "Specify groupsize!" 1>&2 - exit - fi - elif [ "$1" = "--partsize" ]; then - shift - partsize=`expr "$1" - 0` - if ! expr "$1" : "[0-9]" > /dev/null ; then - echo "Specify partsize!" 1>&2 - exit - fi - elif [ "$1" = "--parttree" ]; then - distance="parttree" - partdist="ktuples" - elif [ "$1" = "--dpparttree" ]; then - distance="parttree" - partdist="localalign" - elif [ "$1" = "--fastaparttree" ]; then - distance="parttree" - partdist="fasta" - elif [ "$1" = "--treeout" ]; then - treeout=1 - elif [ "$1" = "--nodeout" ]; then - nodeout=1 - treeout=1 - elif [ "$1" = "--distout" ]; then - distout=1 - elif [ "$1" = "--fastswpair" ]; then - distance="fasta" - pairspecified=1 - sw=1 - elif [ "$1" = "--fastapair" ]; then - distance="fasta" - pairspecified=1 - sw=0 - elif [ "$1" = "--averagelinkage" ]; then - treealg=" -X 1.0 " - sueff="1.0" - elif [ "$1" = "--minimumlinkage" ]; then - treealg=" -X 0.0 " - sueff="0.0" - elif [ "$1" = "--mixedlinkage" ]; then - shift - sueff="$1" - treealg=" -X $1" - elif [ "$1" = "--maxambiguous" ]; then - shift - maxambiguous="$1" - dofilter=1 - elif [ "$1" = "--codonpos" ]; then - shift - codonposfile="$1" - if [ ! -e "$codonposfile" ]; then - echo "Cannot open $codonposfile" 1>&2 - echo "" 1>&2 - exit - fi - codonposopt=" -R " - elif [ "$1" = "--codonscore" ]; then - shift - codonscorefile="$1" - if [ ! -e "$codonscorefile" ]; then - echo "Cannot open $codonscorefile" 1>&2 - echo "" 1>&2 - exit - fi - codonscoreopt=" -S " - elif [ "$1" = "--noscore" ]; then - scorecalcopt=" -Z " - elif [ "$1" = "--6mermultipair" ]; then - distance="ktuplesmulti" - tuplesize=6 - pairspecified=1 - elif [ "$1" = "--10mermultipair" ]; then - distance="ktuplesmulti" - tuplesize=10 - pairspecified=1 - elif [ "$1" = "--6merpair" ]; then - distance="ktuples" - tuplesize=6 - pairspecified=1 - elif [ "$1" = "--10merpair" ]; then - distance="ktuples" - tuplesize=10 - pairspecified=1 - elif [ "$1" = "--blastpair" ]; then - distance="blast" - pairspecified=1 - elif [ "$1" = "--lastmultipair" ]; then - distance="lastmulti" - pairspecified=1 - elif [ "$1" = "--globalpair" ]; then - distance="global" - pairspecified=1 - elif [ "$1" = "--shortlongpair" ]; then - distance="local" - usenaivepairscore="-Z" - laof=0.0 # addfull no tokini tsukawareru. - lexp=0.0 # addfull no tokini tsukawareru. - pgaof=0.0 # local nara iranai - pgexp=0.0 # local nara iranai - pairspecified=1 - elif [ "$1" = "--longshortpair" ]; then - distance="local" - usenaivepairscore="-Z" - laof=0.0 # addfull no tokini tsukawareru. - lexp=0.0 # addfull no tokini tsukawareru. - pgaof=0.0 # local nara iranai - pgexp=0.0 # local nara iranai - pairspecified=1 - elif [ "$1" = "--localpair" ]; then - distance="local" - pairspecified=1 - elif [ "$1" = "--lastpair" ]; then - distance="last" - pairspecified=1 - elif [ "$1" = "--multipair" ]; then - distance="multi" - pairspecified=1 - elif [ "$1" = "--hybridpair" ]; then - distance="hybrid" - pairspecified=1 - elif [ "$1" = "--scarnapair" ]; then - distance="scarna" - pairspecified=1 - elif [ "$1" = "--dafspair" ]; then - distance="dafs" - pairspecified=1 - elif [ "$1" = "--larapair" ]; then - distance="lara" - pairspecified=1 - elif [ "$1" = "--slarapair" ]; then - distance="slara" - pairspecified=1 - elif [ "$1" = "--foldalignpair" ]; then - distance="foldalignlocal" - pairspecified=1 - elif [ "$1" = "--foldalignlocalpair" ]; then - distance="foldalignlocal" - pairspecified=1 - elif [ "$1" = "--foldalignglobalpair" ]; then - distance="foldalignglobal" - pairspecified=1 - elif [ "$1" = "--globalgenafpair" ]; then - distance="globalgenaf" - pairspecified=1 - echo "" 1>&2 - echo "--globalgenaf is no longer supported!" 1>&2 - echo "" 1>&2 - exit 1; - elif [ "$1" = "--localgenafpair" ]; then - distance="localgenaf" - pairspecified=1 - elif [ "$1" = "--genafpair" ]; then - distance="localgenaf" - pairspecified=1 - elif [ "$1" = "--oldgenafpair" ]; then - distance="localgenaf" - pairspecified=1 - oldgenafparam=1 - elif [ "$1" = "--memsave" ]; then - memopt=" -M -B " # -B (bunkatsunashi no riyu ga omoidasenai) - elif [ "$1" = "--nomemsave" ]; then - memopt=" -N " - elif [ "$1" = "--nuc" ]; then - seqtype="-D" # Deleted space, 2018/Dec - elif [ "$1" = "--amino" ]; then - seqtype="-P" # Deleted space, 2018/Dec - elif [ "$1" = "--fft" ]; then - fft=1 - forcefft=1 - elif [ "$1" = "--nofft" ]; then - fft=0 - elif [ "$1" = "--quiet" ]; then -# if [ $os = "msys" ]; then -# progressfile="nul" -# else - progressfile="/dev/null" -# fi - elif [ "$1" = "--debug" ]; then - debug=1 - elif [ "$1" = "--coreext" ]; then - coreext=" -c " - elif [ "$1" = "--core" ]; then - coreout=1 - elif [ "$1" = "--adjustdirection" ]; then - adjustdirection=1 - elif [ "$1" = "--adjustdirectionaccurately" ]; then - adjustdirection=2 - elif [ "$1" = "--oneiteration" ]; then - oneiterationopt=" -r " - elif [ "$1" = "--progress" ]; then - shift - progressfile="$1" - if ! ( expr "$progressfile" : "\/" > /dev/null || expr "$progressfile" : "[A-Za-z]\:" > /dev/null ) ; then - echo "Specify a progress file name with the absolute path!" 1>&2 - exit - fi - elif [ "$1" = "--out" ]; then - shift - outputfile="$1" - elif [ "$1" = "--skipanchorsremoterthan" ]; then - shift - if ! expr "$1" : "[0-9]" > /dev/null ; then - echo "Specify maximum gap length between anchors." 1>&2 - exit - fi - maxanchorseparation=`expr "$1" - 0` - elif [ "$1" = "--anchors" ]; then - shift - anchorfile="$1" - anchoropt=" -l " -# memopt=" -M -B " # ato de kentou -# memopt=" -N " # no memsave - if [ ! -e "$anchorfile" ]; then - echo "Cannot open $anchorfile" 1>&2 - echo "" 1>&2 - exit - fi - elif [ "$1" = "--thread" ]; then - shift - if ! expr "$1" : "[0-9\-]" > /dev/null ; then - echo "Specify the number of threads. Or, use --thread -1" 1>&2 - exit - fi - numthreads=`expr "$1" - 0` - elif [ "$1" = "--threadtb" ]; then - shift - if ! expr "$1" : "[0-9\-]" > /dev/null ; then - echo "Check the argument after --threadtb, the number of threads for the progressive step." 1>&2 - exit - fi - numthreadstb=`expr "$1" - 0` - elif [ "$1" = "--threadit" ]; then - shift - if ! expr "$1" : "[0-9\-]" > /dev/null ; then - echo "Check the argument after --threadit, the number of threads for the iterative step." 1>&2 - exit - fi - numthreadsit=`expr "$1" - 0` - elif [ "$1" = "--last_subopt" ]; then - last_subopt="-S" - elif [ "$1" = "--last_once" ]; then - last_once="-U" - elif [ "$1" = "--last_m" ]; then - shift - last_m=`expr "$1" - 0` - elif [ "$1" = "--last_e" ]; then - shift - last_e=`expr "$1" - 0` - elif [ "$1" = "--randomseed" ]; then - shift - randomseed=`expr "$1" - 0` - elif [ "$1" = "--bestfirst" ]; then - parallelizationstrategy="BESTFIRST" - elif [ "$1" = "--adhoc0" ]; then - parallelizationstrategy="BAATARI0" - elif [ "$1" = "--adhoc1" ]; then - parallelizationstrategy="BAATARI1" - elif [ "$1" = "--adhoc2" ]; then - parallelizationstrategy="BAATARI2" - elif [ "$1" = "--simplehillclimbing" ]; then - parallelizationstrategy="BAATARI2" - elif [ "$1" = "--scoreout" ]; then - scoreoutarg="-S -B" - elif [ "$1" = "--outnum" ]; then - outnum="-n" - elif [ "$1" = "--leavegappyregion" ]; then - legacygapopt="-L" - elif [ "$1" = "--legacygappenalty" ]; then - legacygapopt="-L" - elif [ "$1" = "--merge" ]; then - shift - mergetable="$1" - if [ ! -e "$mergetable" ]; then - echo "Cannot open $mergetable" 1>&2 - echo "" 1>&2 - exit - fi - elif [ "$1" = "--addprofile" ]; then - shift - addarg0="-I" - addfile="$1" - elif [ "$1" = "--add" ]; then - shift - addarg0="-K -I" - addfile="$1" - elif [ "$1" = "--addfragments" ]; then - shift - addarg0="-K -I" - addfile="$1" - fragment=1 - elif [ "$1" = "--addfull" ]; then - shift - addarg0="-K -I" - addfile="$1" - fragment=-1 - elif [ "$1" = "--addlong" ]; then - shift - addarg0="-K -I" - addfile="$1" - fragment=-2 - elif [ "$1" = "--addtotop" ]; then - shift - addarg0="-K -I" - addfile="$1" - fragment=-3 - elif [ "$1" = "--addtoroot" ]; then - shift - addarg0="-K -I" - addfile="$1" - fragment=-4 - elif [ "$1" = "--smoothing" ]; then - add2ndhalfarg=$add2ndhalfarg" -p " - elif [ "$1" = "--keeplength" ]; then - add2ndhalfarg=$add2ndhalfarg" -Y " - elif [ "$1" = "--compactmapout" ]; then - add2ndhalfarg=$add2ndhalfarg" -z -Y " - elif [ "$1" = "--compactmapoutfile" ]; then - shift - add2ndhalfarg=$add2ndhalfarg" -z -Y " - mapoutfile="$1" - elif [ "$1" = "--mapout" ]; then - add2ndhalfarg=$add2ndhalfarg" -Z -Y " - elif [ "$1" = "--mapoutfile" ]; then - shift - add2ndhalfarg=$add2ndhalfarg" -Z -Y " - mapoutfile="$1" - elif [ "$1" = "--maxiterate" ]; then - shift - iterate=`expr "$1" - 0` - if ! expr "$1" : "[0-9]" > /dev/null ; then - echo "Specify the number of iterations!" 1>&2 - exit - fi - elif [ "$1" = "--retree" ]; then - shift - cycle=`expr "$1" - 0` - if ! expr "$1" : "[0-9]" > /dev/null ; then - echo "Specify the number of tree rebuilding!" 1>&2 - exit - fi - elif [ "$1" = "--aamatrix" ]; then - shift - f2clext="-N" - sbstmodel=" -b -1 " - scorematrix="$1" - if [ ! -e "$scorematrix" ]; then - echo "Cannot open $scorematrix" 1>&2 - echo "" 1>&2 - exit - fi - elif [ "$1" = "--textmatrix" ]; then - shift - f2clext="-E" - seqtype="-P" - fft=0 -# sbstmodel=" -b -2 -a " - sbstmodel=" -b -2 " # 2022/Jul, hauretsu no kawari ni scoremtx wo miru - scorematrix="$1" - if [ ! -e "$scorematrix" ]; then - echo "Cannot open $scorematrix" 1>&2 - echo "" 1>&2 - exit - fi - elif [ "$1" = "--text" ]; then - f2clext="-E" - seqtype="-P" - fft=0 - sbstmodel=" -b -2 -a " - elif [ "$1" = "--treein" ]; then - shift - treeinopt=" -U " - treein=1 - treeinfile="$1" - if [ ! -e "$treeinfile" ]; then - echo "Cannot open $treeinfile" 1>&2 - echo "" 1>&2 - exit - fi - elif [ "$1" = "--pileup" ]; then -# treeinopt=" -U " -# treein=1 - treeext="pileup" - elif [ "$1" = "--randomchain" ]; then -# treeinopt=" -U " -# treein=1 -# pileuporshuffle="s" - treeext="randomchain" - elif [ "$1" = "--topin" ]; then - shift - treeinopt=" -V " - treein=1 - treeinfile="$1" - echo "The --topin option has been disabled." 1>&2 - echo "There was a bug in version < 6.530." 1>&2 - echo "This bug has not yet been fixed." 1>&2 - exit 1 - elif [ "$1" = "--mpi" ]; then - mpiscript="$prefix/mpiscript" - elif [ "$1" = "--large" ]; then - treeext="memsavetree" - elif [ "$1" = "--memsavetree" ]; then - treeext="memsavetree" - elif [ "$1" = "--memsavetreex" ]; then - treeext="memsavetreex" - elif [ "$1" = "--stepadd" ]; then - treeext="stepadd" - elif [ "$1" = "--youngestlinkage" ]; then - treeext="youngestlinkage" - elif [ "$1" = "--kappa" ]; then - shift - kappa=" -k $1 " - if ! expr "$1" : "[0-9]" > /dev/null ; then - echo "Specify kappa value!" 1>&2 - exit - fi - elif [ "$1" = "--fmodel" ]; then - fmodel=" -a " - elif [ "$1" = "--nwildcard" ]; then - nmodel=" -: " - elif [ "$1" = "--nzero" ]; then - nmodel=" " - elif [ "$1" = "--jtt" ]; then - shift - f2clext="-N" - sbstmodel=" -j $1" -# if ! expr "$1" : "[0-9]" > /dev/null ; then -# echo "Specify pam value!" 1>&2 -# exit -# fi - elif [ "$1" = "--kimura" ]; then - shift - f2clext="-N" - sbstmodel=" -j $1" -# if ! expr "$1" : "[0-9]" > /dev/null ; then -# echo "Specify pam value!" 1>&2 -# exit -# fi - elif [ "$1" = "--tm" ]; then - shift - f2clext="-N" - sbstmodel=" -m $1" -# if ! expr "$1" : "[0-9]" > /dev/null ; then -# echo "Specify pam value!" 1>&2 -# exit -# fi - elif [ "$1" = "--bl" ]; then - shift - f2clext="-N" - sbstmodel=" -b $1" - if ! expr "$1" : "[0-9]" > /dev/null ; then - echo "blosum $1?" 1>&2 - exit - fi - elif [ "$1" = "--weighti" ]; then - shift - weighti="$1" - if ! expr "$1" : "[0-9]" > /dev/null ; then - echo "Specify weighti value!" 1>&2 - exit - fi - elif [ "$1" = "--weightr" ]; then - shift - weightr="$1" - if ! expr "$1" : "[0-9]" > /dev/null ; then - echo "Specify weightr value!" 1>&2 - exit - fi - elif [ "$1" = "--weightm" ]; then - shift - weightm="$1" - if ! expr "$1" : "[0-9]" > /dev/null ; then - echo "Specify weightm value!" 1>&2 - exit - fi - elif [ "$1" = "--rnaalifold" ]; then - rnaalifold=1 - elif [ "$1" = "--mccaskill" ]; then - mccaskill=1 - contrafold=0 - dafs=0 - elif [ "$1" = "--contrafold" ]; then - mccaskill=0 - contrafold=1 - dafs=0 - elif [ "$1" = "--dafs" ]; then - mccaskill=0 - contrafold=0 - dafs=1 - elif [ "$1" = "--ribosum" ]; then - rnascoremtx=" -s " - elif [ "$1" = "--op" ]; then - shift - gop="$1" - if ! expr "$1" : "[0-9]" > /dev/null ; then - echo "Specify op!" 1>&2 - exit - fi - elif [ "$1" = "--opdist" ]; then - shift - gopdist="$1" - if ! expr "$1" : "[0-9]" > /dev/null ; then - echo "Specify opdist!" 1>&2 - exit - fi - opdistspecified=1 - elif [ "$1" = "--allowshift" ]; then - allowshift=1 - elif [ "$1" = "--shiftpenalty" ]; then - shift - spfactor="$1" - if ! expr "$1" : "[0-9]" > /dev/null ; then - echo "Specify sf!" 1>&2 - exit - fi - shiftpenaltyspecified=1 - elif [ "$1" = "--exp" ]; then - shift -# gexp="$1" - tmpval="$1" - gexp=`awk "BEGIN{ print -1.0 * \"$tmpval\"}"` - if ! expr "$gexp" : "[0-9\-]" > /dev/null ; then - printf "\nSpecify a number for exp, like --exp 0.1\n" 1>&2 - printf "'$1' cannot be interpreted as a number..\n\n" 1>&2 - exit - fi - elif [ "$1" = "--ep" ]; then - shift -# aof="$1" - tmpval="$1" - aof=`awk "BEGIN{ print -1.0 * \"$tmpval\"}"` - if ! expr "$aof" : "[0-9\-]" > /dev/null ; then - printf "\nSpecify a number for ep, like --ep 0.1\n" 1>&2 - printf "'$1' cannot be interpreted as a number..\n\n" 1>&2 - exit - fi - elif [ "$1" = "--rop" ]; then - shift - rgop="$1" -# Atode check - elif [ "$1" = "--rep" ]; then - shift - rgep="$1" - elif [ "$1" = "--lop" ]; then - shift - lgop="$1" - elif [ "$1" = "--LOP" ]; then - shift - LGOP="$1" - elif [ "$1" = "--lep" ]; then - shift - laof="$1" - elif [ "$1" = "--lexp" ]; then - shift - lexp="$1" - elif [ "$1" = "--LEXP" ]; then - shift - LEXP="$1" - elif [ "$1" = "--GEXP" ]; then - shift - GEXP="$1" - elif [ "$1" = "--GOP" ]; then - shift - GGOP="$1" - elif [ "$1" = "--gop" ]; then - shift - pggop="$1" - elif [ "$1" = "--gep" ]; then - shift - pgaof="$1" - elif [ "$1" = "--gexp" ]; then - shift - pgexp="$1" - elif [ "$1" = "--laraparams" ]; then - shift - laraparams="$1" - elif [ "$1" = "--corethr" ]; then - shift - corethr="$1" - elif [ "$1" = "--corewin" ]; then - shift - corewin="$1" - elif [ "$1" = "--strdir" ]; then - shift - strdir="$1" - elif [ "$1" = "--pdbidlist" ]; then - echo "--pdbidlist is temporarily unavailable, 2018/Dec." 1>&2 - echo "" 1>&2 - exit - shift - pdblist="$1" - if [ ! -e "$pdblist" ]; then - echo "Cannot open $pdblist" 1>&2 - echo "" 1>&2 - exit - fi - elif [ "$1" = "--pdbfilelist" ]; then - echo "--pdbfilelist is temporarily unavailable, 2018/Dec." 1>&2 - echo "" 1>&2 - exit - shift - ownlist="$1" - if [ ! -e "$ownlist" ]; then - echo "Cannot open $ownlist" 1>&2 - echo "" 1>&2 - exit - fi -# elif [ "$1" = "--enrich" ]; then -# enrich=1 -# enrichseq=1 -# enrichstr=1 -# seektarget="" -# elif [ "$1" = "--enrichseq" ]; then -# enrich=1 -# enrichseq=1 -# enrichstr=0 -# seektarget="-seq" -# elif [ "$1" = "--enrichstr" ]; then -# enrich=1 -# enrichseq=0 -# enrichstr=1 -# seektarget="-str" - elif [ "$1" = "--dash" ]; then - newdash=1 - if [ "$distance" != "local" -a "$distance" != "localgenaf" ]; then # 2021/Oct - distance="global" - fi - if [ "$iterate" -eq 0 ]; then # 2021/Oct - iterate=3 - fi - elif [ "$1" = "--dashserver" ]; then - shift - dashserver="$1" - elif [ "$1" = "--originalseqonly" ]; then - newdash_originalsequenceonly=1 - elif [ "$1" = "--excludehomologs" ]; then # works with --dash only - exclude_ho=1 - elif [ "$1" = "--seedtable" ]; then - shift - seedtable="y" - seedtablefile="$1" - elif [ "$1" = "--seed" ]; then - shift - seed="m" - seedfiles="$seedfiles $1" - elif [ "$1" = "--minimumweight" ]; then - shift - minimumweight="$1" - elif [ "$1" = "--similaritylevel" ]; then - shift - similarityoffset="$1" - elif [ "$1" = "--unalignlevel" ]; then - shift - unalignlevel="$1" - unalignspecified=1 - elif [ "$1" = "--skipiterate" ]; then - shift - fixthreshold="$1" - elif [ "$1" = "--bunkatsunashi" ]; then - bunkatsuopt=" -B " - elif [ "$1" = "--sp" ]; then - sprigorous=1 - elif [ "$1" = "--focus" ]; then - focusarg=" -= " - elif [ "$1" = "--lhlimit" ]; then # atode namae henkou - shift - lhlimit=" -q $1 " - elif [ "$1" = "--sparsepickup" ]; then - shift - npickup="$1" - elif [ $progname = "fftns" -o $progname = "nwns" ]; then - if [ "$1" -gt 0 ]; then - cycle=`expr "$1" - 0` - fi - else - echo "Unknown option: $1" 1>&2 - er=1; -# exit 1; - fi - shift - done; - - -# echo "" 1>"$progressfile" - - if [ $treeext = "memsavetree" ] || [ $treeext = "stepadd" ]; then - if [ $distance != "ktuples" ]; then -# auto -> memsave && globalpair ha erabarenai node, -# ~/maffttmp wo tsukau noha meijiteki ni shitei saretatoki dake. - if [ ! "$MAFFT_TMPDIR" ]; then # space is acceptable, 2018/Mar/17 - MAFFT_TMPDIR="$HOME/maffttmp" - mkdir -p "$MAFFT_TMPDIR" || exit - fi - fi - fi - - - if [ ! "$MAFFT_TMPDIR" ]; then - MAFFT_TMPDIR="$TMPDIR" - fi - - TMPFILE=`env TMPDIR="$MAFFT_TMPDIR" mktemp -dt "$progname.XXXXXXXXXX"` - if [ $? -ne 0 ]; then - echo "mktemp seems to be obsolete. Re-trying without -t" 1>&2 - mkdir -p "$MAFFT_TMPDIR/tmp" 1>&2 - TMPFILE=`mktemp -d "$MAFFT_TMPDIR/tmp/$progname.XXXXXXXXXX"` - fi - -# lfs getstripe $TMPFILE 2>/dev/null && lfs setstripe -c 1 $TMPFILE # 2017/Oct - lfs getstripe "$TMPFILE" > /dev/null 2>&1 && lfs setstripe -c 1 "$TMPFILE" > /dev/null 2>&1 # 2018/Feb - - if [ $os = "cygwin" ]; then - TMPFILE=`cygpath -w "$TMPFILE"` # necessary to pass path to f2cl on cyswin, somehow unnecessary in msys. - fi - -# umask 077 # 2021/Jan -# mkdir "$TMPFILE" || er=1 - - -function removetmpfile() { # for MPI - while true - do - rm -rf "$TMPFILE" && break - echo Retrying to remove "$TMPFILE". It may take several seconds. 1>&2 - sleep 2 - done -} - - if [ $debug -eq 1 ]; then -# trap "tar cfvz debuginfo.tgz $TMPFILE; rm -rf $TMPFILE " 0 # does not work in msys -# trap "tar cfv - $TMPFILE | gzip -c > debuginfo.tgz; rm -rf $TMPFILE " 0 15 - trap "popd > /dev/null 2>&1; tar cfv - \"$TMPFILE\" | gzip -c > debuginfo.tgz; removetmpfile" 0 15 - else -# trap "rm -rf $TMPFILE" 0 15 - trap "removetmpfile" 0 15 - fi - if [ $# -eq 1 ]; then - if [ -r "$1" -o "$1" = - ]; then - - if [ -r "$addfile" ]; then - printf ''; - else - echo "$0": Cannot open "$addfile". 1>&2 - echo "" 1>&2 - exit 1; - fi - - - cat "$1" | tr "\r" "\n" > "$TMPFILE/infile" - echo "" >> "$TMPFILE/infile" - cat "$addfile" | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/_addfile" - - if [ $dofilter -eq 1 ]; then -# mv "$TMPFILE/infile" "$TMPFILE/_tofilter" -# "$prefix/filter" -m $maxambiguous $seqtype -i "$TMPFILE/_tofilter" > "$TMPFILE/infile" 2>>"$progressfile" || exit 1 - mv "$TMPFILE/_addfile" "$TMPFILE/_tofilter" - "$prefix/filter" -m $maxambiguous $seqtype -i "$TMPFILE/_tofilter" > "$TMPFILE/_addfile" 2>>"$progressfile" || exit 1 - fi - cat "$TMPFILE/_addfile" >> "$TMPFILE/infile" - - cat "$scorematrix" | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/_aamtx" - cat "$mergetable" | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/_subalignmentstable" - cat "$treeinfile" | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/_guidetree" - cat "$codonposfile" | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/_codonpos" - cat "$codonscorefile" | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/_codonscore" - cat "$seedtablefile" | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/_seedtablefile" - cat "$laraparams" | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/_lara.params" - cat "$pdblist" | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/pdblist" - cat "$ownlist" | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/ownlist" - cat "$anchorfile" | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/_externalanchors" - - SAVEIFS=$IFS -# Fixed a bug: 'n' was misinterpreted as delimiter, 2020/Jun/19 - IFS=$'\n' - filelist="$1 -$addfile -$scorematrix -$mergetable -$treeinfile -$codonposfile -$codonscorefile -$seedtablefile -$laraparams -$pdblist -$ownlist" - for f in $filelist; do - file "$f" 2>/dev/null | grep -e 'UTF-16' -e 'UTF-32' >& /dev/null && printf "$f: UTF-16 or UTF-32? Convert this file to ASCII\n\n" 1>&2 && exit 1; - done - IFS=$SAVEIFS - -# echo $seedfiles - infilename="$1" - seedfilesintmp="/dev/null" - seednseq="0" - set $seedfiles > /dev/null - while [ $# -gt 1 ]; - do - shift - if [ -r "$1" ]; then - cat "$1" | tr "\r" "\n" > "$TMPFILE/seed$#" - file "$1" | grep -e 'UTF-16' -e 'UTF-32' >& /dev/null && printf "$1: UTF-16 or UTF-32? Convert this file to ASCII\n\n" 1>&2 && exit 1; - else - echo "$0": Cannot open "$1". 1>&2 - echo "" 1>&2 - exit 1; - fi - seednseq=$seednseq" "`grep -c '^[>|=]' "$TMPFILE/seed$#"` - seedfilesintmp=$seedfilesintmp" "seed$# - done -# ls $TMPFILE -# echo $seedfilesintmp -# echo $seednseq - - - else - echo "$0": Cannot open "$1". 1>&2 - echo "" 1>&2 - er=1 -# exit 1; - fi - else -# echo '$#'"=$#" 1>&2 - er=1 - fi - - - if [ $numthreads -lt 0 ]; then - if [ $os = "linux" ]; then - nlogicalcore=`cat /proc/cpuinfo | grep "^processor" | uniq | wc -l` - ncoresinacpu=`cat /proc/cpuinfo | grep 'cpu cores' | uniq | awk '{print $4}'` - nphysicalcpu=`cat /proc/cpuinfo | grep 'physical id' | sort | uniq | wc -l` - if [ $nlogicalcore -eq 0 ]; then - echo "Cannot get the number of processors from /proc/cpuinfo" 1>>"$progressfile" - exit 1 - fi - if [ ${#ncoresinacpu} -gt 0 -a $nphysicalcpu -gt 0 ]; then - numthreads=`expr $ncoresinacpu '*' $nphysicalcpu` -# if [ $nlogicalcore -gt $numthreads ]; then # Hyperthreading -# numthreads=`expr $numthreads '+' 1` -# fi - else - numthreads=$nlogicalcore - fi - elif [ $os = "darwin" ]; then - numthreads=`sysctl -n hw.physicalcpu` - if [ -z $numthreads ]; then - echo "Cannot get the number of physical cores from sysctl" 1>>"$progressfile" - exit 1 - fi -# nlogicalcore=`sysctl -n hw.logicalcpu` -# if [ $nlogicalcore -gt $numthreads ]; then # Hyperthreading -# numthreads=`expr $numthreads '+' 1` -# fi - elif [ "$windows" = "yes" ]; then -# numthreads=`wmic cpu get NumberOfCores | head -2 | tail -1 | awk '{print $1}'` - numthreads=`wmic cpu get NumberOfCores | awk 'BEGIN{n=0} {n+=$1} END{print n}'` - - else - echo "Cannot count the number of physical cores." 1>>"$progressfile" - exit 1 - fi - echo "OS = "$os 1>>"$progressfile" - echo "The number of physical cores = " $numthreads 1>>"$progressfile" - fi - - if [ $numthreadstb -lt 0 ]; then - if [ $numthreads -lt 16 -o "$mpiscript" != "/dev/null" ]; then # mpi: museigen, multithread: 16 made -# if [ $numthreads -lt 31 ]; then - numthreadstb=$numthreads - else - numthreadstb=16 - fi - fi - - if [ $numthreadsit -lt 0 ]; then - if [ $numthreads -lt 8 ]; then - numthreadsit=$numthreads - else - numthreadsit=8 - fi - fi - - if [ $numthreadsit -eq 0 -a $parallelizationstrategy = "BESTFIRST" ]; then - echo 'Impossible' 1>&2; - exit 1; - fi - - - if [ "$addarg0" != " " ]; then - -# iterate=0 # 2013/03/23 -> commented out, 2017/12 - "$prefix/countlen" < "$TMPFILE/_addfile" > "$TMPFILE/addsize" 2>>"$progressfile" - nadd=`awk '{print $1}' "$TMPFILE/addsize"` - if [ $nadd -eq "0" ]; then - echo Check $addfile 1>&2 - exit 1; - fi - if [ $seed != "x" -o $seedtable != "x" ]; then - echo 'Impossible' 1>&2; - echo 'Use either ONE of --seed, --seedtable, --addprofile and --add.' 1>&2 - exit 1; - fi - else - nadd="0" - fi - - if [ $auto -eq 1 ]; then - "$prefix/countlen" < "$TMPFILE/infile" > "$TMPFILE/size" 2>>"$progressfile" - nseq=`awk '{print $1}' "$TMPFILE/size"` - nlen=`awk '{print $3}' "$TMPFILE/size"` - - if [ $nlen -lt 3000 -a $nseq -lt 100 ]; then - distance="local" - iterate=1000 - cycle=1 - treeext="none" - elif [ $nlen -lt 1000 -a $nseq -lt 200 ]; then - distance="local" - iterate=2 - cycle=1 - treeext="none" - elif [ $nlen -lt 10000 -a $nseq -lt 500 ]; then - distance="ktuples" - iterate=2 - cycle=2 - treeext="none" - elif [ $nseq -lt 20000 ]; then # changed from 10000 2014/Oct/4 - distance="ktuples" - iterate=0 - cycle=2 - treeext="none" - elif [ $nseq -lt 100000 ]; then # changed from 50000 2017/Nov/24 - distance="ktuples" - iterate=0 - cycle=2 - if [ $fragment -eq 0 -a "$mergetable" = "/dev/null" ]; then - treeext="memsavetree" - fi - elif [ $nseq -lt 200000 ]; then # changed from 90000 2017/Nov/24 - distance="ktuples" - iterate=0 - cycle=1 - if [ $fragment -eq 0 -a "$mergetable" = "/dev/null" ]; then - treeext="memsavetree" - fi - elif [ $nlen -lt 3000 ]; then - distance="parttree" - partdist="localalign" - algopt=" " - algoptit=" " -# algspecified=1 - cycle=1 - else - distance="parttree" - partdist="ktuples" - algopt=" " - algoptit=" " -# algspecified=1 - cycle=1 - fi - - -# if [ $nlen -lt 3000 -a $nseq -lt 100 ]; then -# distance="local" -# iterate=1000 -# cycle=1 -# elif [ $nlen -lt 1000 -a $nseq -lt 200 ]; then -# distance="local" -# iterate=2 -# cycle=1 -# elif [ $nlen -lt 10000 -a $nseq -lt 500 ]; then -# distance="ktuples" -# iterate=2 -# cycle=2 -# elif [ $nseq -lt 200000 ]; then -# distance="ktuples" -# iterate=0 -# treeinopt=" -U " -# treein=1 -# pileuporshuffle="a" -# elif [ $nlen -lt 3000 ]; then -# distance="parttree" -# partdist="localalign" -# algopt=" " -# algoptit=" " -## algspecified=1 -# cycle=1 -# else -# distance="parttree" -# partdist="ktuples" -# algopt=" " -# algoptit=" " -## algspecified=1 -# cycle=1 -# fi - - - if [ $fragment -ne 0 ]; then - norg=`expr $nseq '-' $nadd` - npair=`expr $norg '*' $nadd` - echo "nadd = " $nadd 1>>"$progressfile" - echo "npair = " $npair 1>>"$progressfile" - echo "nseq = " $nseq 1>>"$progressfile" - echo "nlen = " $nlen 1>>"$progressfile" - - if [ $norg -eq 0 ]; then - echo "" 1>>"$progressfile" - echo "The reference sequence was removed because of ambiguous letters?" 1>>"$progressfile" - echo "" 1>>"$progressfile" - exit 1; - fi -# nagasa check! -# if [ $npair -gt 10000000 -o $nlen -gt 5000 ]; then # 2017/Oct - if [ $npair -gt 10000000 -o $nlen -gt 5000 -o $nadd -gt 500000 ]; then # 2021/Dec pairlocalalign to buntan - distance="ktuples" - echo "use ktuples, size=$tuplesize!" 1>>"$progressfile" -# elif [ $npair -gt 3000000 -o $nlen -gt 5000 ]; then # 2017/Oct - elif [ $npair -gt 3000000 -o $nlen -gt 5000 ]; then # 2017/Oct - distance="multi" - weighti="0.0" - echo "use multipair, weighti=0.0!" 1>>"$progressfile" - else - distance="multi" - echo "use multipair, weighti=$weighti!" 1>>"$progressfile" - fi - pairspecified=1 - fi - fi - - if [ `awk "BEGIN {print( 0.0+\"$sueff\" < 0.0 || 0.0+\"$sueff\" > 1.0 )}"` -gt 0 ]; then - printf "\n%s\n\n" "The argument of --mixedlinkage must be between 0.0 and 1.0" 1>>"$progressfile" - exit 1; - fi - - if [ `awk "BEGIN {print( 0.0+\"$maxambiguous\" < 0.0 || 0.0+\"$maxambiguous\" > 1.0 )}"` -gt 0 ]; then - printf "\n%s\n\n" "The argument of --maxambiguous must be between 0.0 and 1.0" 1>>"$progressfile" - exit 1; - fi - - if [ $allowshift -eq 1 ]; then - if [ $unalignspecified -ne 1 ]; then - unalignlevel="0.8" - fi - if [ $shiftpenaltyspecified -ne 1 ]; then - spfactor="2.00" - fi - fi - - if [ $opdistspecified -ne 1 ]; then - gopdist=$gop - fi - - if [ $unalignlevel != "0.0" -o `awk "BEGIN {print( 0.0+\"$spfactor\" < 100.0 )}"` -gt 0 ]; then - nmodel=" -: " - termgapopt=" " - if [ $distance = "localgenaf" ]; then - printf "\n%s\n" "The combination of --allowshift and --genafpair (E-INS-i/-1) is not supported." 1>>"$progressfile" - printf "%s\n" "Instead, please try --allowshift --globalpair (G-INS-i/-1 in the web version)," 1>>"$progressfile" - printf "%s\n\n" "which covers the situation for --genafpair (E-INS-i/-1), too." 1>>"$progressfile" - exit 1; - fi - if [ $distance != "global" -o `awk "BEGIN {print( 0.0+\"$weighti\" < 1.0 )}"` -gt 0 ]; then - printf "\n%s\n\n" "At present, --unalignlevel # or --allowshift is supported only with the --globalpair option." 1>>"$progressfile" - exit 1; - fi - if [ $fragment -ne 0 ]; then - printf "\n%s\n\n" "At present, --unalignlevel # or --allowshift is not supported with the --addfragments option." 1>>"$progressfile" - exit 1; - fi - fi - - if [ `awk "BEGIN {print( 0.0+\"$spfactor\" < 1.0 )}"` -gt 0 ]; then - printf "\n%s\n" "shiftpenalty must be >1." 1>>"$progressfile" - exit 1; - fi - - if [ `awk "BEGIN {print( 0.0+\"$fixthreshold\" < 0.0 )}"` -gt 0 ]; then - printf "\n%s\n\n" "The 'fix' parameter must be >= 0.0" 1>>"$progressfile" - exit 1; - fi - - if [ `awk "BEGIN {print( 0.0+\"$unalignlevel\" < 0.0 || 0.0+\"$unalignlevel\" > 1.0 )}"` -gt 0 ]; then - printf "\n%s\n\n" "The 'unalignlevel' parameter must be between 0.0 and 1.0" 1>>"$progressfile" - exit 1; - fi - if [ `awk "BEGIN {print( 0.0+\"$unalignlevel\" > 0.0 )}"` -gt 0 ]; then - laof="0" - lexp="0" - pgaof="0" - pgexp="0" - LEXP="0" - GEXP="0" - termgapopt=" " -# if [ $auto -eq 1 -o $fragment -ne 0 -o $iterate -gt 0 ]; then - if [ $fragment -ne 0 ]; then - printf "\n%s\n\n" "At present, the 'unalignlevel > 0' mode is not supported with the --addfragments option." 1>>"$progressfile" - exit 1; - fi - if [ $distance = "parttree" ]; then - printf "\n%s\n\n" "At present, the 'unalignlevel > 0' mode is not supported in the (dp)parttree option." 1>>"$progressfile" - exit 1; - fi - if [ $distance = "localgenaf" ]; then - printf "\n%s\n" "The --genafpair is not supported in the 'unalignlevel > 0' mode." 1>>"$progressfile" - printf "%s\n" "Instead, please try --unalignlevel xx --globalpair," 1>>"$progressfile" - printf "%s\n\n" "which covers the situation for --genafpair (E-INS-i), too." 1>>"$progressfile" - exit 1; - fi -# if [ $distance != "ktuples" -a `awk "BEGIN {print( 0.0+\"$weighti\" > 0.0 )}"` -gt 0 -a $iterate -gt 0 ]; then -# printf "\n%s\n\n" "Please add --weighti 0.0, for now." 1>>"$progressfile" -# exit 1; -# fi - fi - - if [ `awk "BEGIN {print( 0.0+\"$similarityoffset\" != 0.0 && 0.0+\"$unalignlevel\" != 0.0 )}"` -gt 0 ]; then - printf "\n%s\n\n" "Do not simultaneously specify --similaritylevel and --unalignlevel" 1>>"$progressfile" - exit 1; - fi - - if [ `awk "BEGIN {print( 0.0+\"$similarityoffset\" < -1.0 || 0.0+\"$similarityoffset\" > 1.0 )}"` -gt 0 ]; then - printf "\n%s\n\n" "Similarity must be between -1.0 and +1.0" 1>>"$progressfile" - exit 1; - fi - aof=`awk "BEGIN{print 0.0 + \"$similarityoffset\" + $aof}"` - laof=`awk "BEGIN{print 0.0 + \"$similarityoffset\" + $laof}"` - pgaof=`awk "BEGIN{print 0.0 + \"$similarityoffset\" + $pgaof}"` - - - if [ $parallelizationstrategy = "BESTFIRST" -o $parallelizationstrategy = "BAATARI0" ]; then - iteratelimit=254 - else - iteratelimit=16 - fi - if [ $iterate -gt $iteratelimit ]; then #?? - iterate=$iteratelimit - fi - - if [ $rnaalifold -eq 1 ]; then - rnaopt=" -e $rgep -o $rgop -c $weightm -r $weightr -R $rnascoremtx " -# rnaoptit=" -o $rgop -BT -c $weightm -r $weightr -R " - rnaoptit=" -o $rgop -F -c $weightm -r $weightr -R " - elif [ $mccaskill -eq 1 -o $dafs -eq 1 -o $contrafold -eq 1 ]; then - rnaopt=" -o $rgop -c $weightm -r $weightr " -# rnaoptit=" -e $rgep -o $rgop -BT -c $weightm -r $weightr $rnascoremtx " - rnaoptit=" -e $rgep -o $rgop -F -c $weightm -r $weightr $rnascoremtx " - else - rnaopt=" " - rnaoptit=" -F " - fi - -# if [ $algspecified -eq 0 ]; then -# if [ $distance = "parttree" ]; then -# algopt=" -Q " -# algoptit=" " -# else -# algopt=" " -# algoptit=" " -# fi -# fi - - if [ $sprigorous -eq 1 ]; then - algopt=" -@ " - if [ $iterate -gt 0 ]; then - if [ $numthreadsit -eq 0 ]; then - algoptit=" -@ -B -Z -z 1000 " - else - echo "" 1>>"$progressfile" - echo "At present, the combination of --sp and iterative refinement is supported only in a single thread." 1>>"$progressfile" - echo "Please try \"--thread -1 --threadit 0\", which runs the iterative refinment calculation on a single thread." 1>>"$progressfile" - echo "" 1>>"$progressfile" - exit 1; -# algoptit=" -@ -B -z 1000 " - fi - fi - termgapopt=" " - fft=0 - memopt=" -N " - fi - - model="$sbstmodel $kappa $fmodel $nmodel" - - if [ $er -eq 1 ]; then - echo "------------------------------------------------------------------------------" 1>&2 - echo " MAFFT" $version 1>&2 -# echo "" 1>&2 -# echo " Input format: fasta" 1>&2 -# echo "" 1>&2 -# echo " Usage: `basename $0` [options] inputfile > outputfile" 1>&2 - echo " https://mafft.cbrc.jp/alignment/software/" 1>&2 - echo " MBE 30:772-780 (2013), NAR 30:3059-3066 (2002)" 1>&2 -# echo "------------------------------------------------------------------------------" 1>&2 -# echo " % mafft in > out" 1>&2 - echo "------------------------------------------------------------------------------" 1>&2 -# echo "" 1>&2 - echo "High speed:" 1>&2 - echo " % mafft in > out" 1>&2 - echo " % mafft --retree 1 in > out (fast)" 1>&2 - echo "" 1>&2 - echo "High accuracy (for <~200 sequences x <~2,000 aa/nt):" 1>&2 - echo " % mafft --maxiterate 1000 --localpair in > out (% linsi in > out is also ok)" 1>&2 - echo " % mafft --maxiterate 1000 --genafpair in > out (% einsi in > out)" 1>&2 - echo " % mafft --maxiterate 1000 --globalpair in > out (% ginsi in > out)" 1>&2 - echo "" 1>&2 - echo "If unsure which option to use:" 1>&2 - echo " % mafft --auto in > out" 1>&2 - echo "" 1>&2 -# echo "Other options:" 1>&2 - echo "--op # : Gap opening penalty, default: 1.53" 1>&2 - echo "--ep # : Offset (works like gap extension penalty), default: 0.0" 1>&2 - echo "--maxiterate # : Maximum number of iterative refinement, default: 0" 1>&2 - echo "--clustalout : Output: clustal format, default: fasta" 1>&2 - echo "--reorder : Outorder: aligned, default: input order" 1>&2 - echo "--quiet : Do not report progress" 1>&2 - echo "--thread # : Number of threads (if unsure, --thread -1)" 1>&2 - echo "--dash : Add structural information (Rozewicki et al, submitted)" 1>&2 -# echo "" 1>&2 -# echo " % mafft --maxiterate 1000 --localpair in > out (L-INS-i)" 1>&2 -# echo " most accurate in many cases, assumes only one alignable domain" 1>&2 -# echo "" 1>&2 -# echo " % mafft --maxiterate 1000 --genafpair in > out (E-INS-i)" 1>&2 -# echo " works well if many unalignable residues exist between alignable domains" 1>&2 -# echo "" 1>&2 -# echo " % mafft --maxiterate 1000 --globalpair in > out (G-INS-i)" 1>&2 -# echo " suitable for globally alignable sequences " 1>&2 -# echo "" 1>&2 -# echo " % mafft --maxiterate 1000 in > out (FFT-NS-i)" 1>&2 -# echo " accurate and slow, iterative refinement method " 1>&2 -# echo "" 1>&2 -# echo "If the input sequences are long (~1,000,000nt)," 1>&2 -# echo " % mafft --retree 1 --memsave --fft in > out (FFT-NS-1-memsave, new in v5.8)" 1>&2 -# echo "" 1>&2 -# echo "If many (~5,000) sequences are to be aligned," 1>&2 -# echo "" 1>&2 -# echo " % mafft --retree 1 [--memsave] --nofft in > out (NW-NS-1, new in v5.8)" 1>&2 -# echo "" 1>&2 -# echo " --localpair : All pairwise local alignment information is included" 1>&2 -# echo " to the objective function, default: off" 1>&2 -# echo " --globalpair : All pairwise global alignment information is included" 1>&2 -# echo " to the objective function, default: off" 1>&2 -# echo " --op # : Gap opening penalty, default: $defaultgop " 1>&2 -# echo " --ep # : Offset (works like gap extension penalty), default: $defaultaof " 1>&2 -# echo " --bl #, --jtt # : Scoring matrix, default: BLOSUM62" 1>&2 -# echo " Alternatives are BLOSUM (--bl) 30, 45, 62, 80, " 1>&2 -# echo " or JTT (--jtt) # PAM. " 1>&2 -# echo " --nuc or --amino : Sequence type, default: auto" 1>&2 -# echo " --retree # : The number of tree building in progressive method " 1>&2 -# echo " (see the paper for detail), default: $defaultcycle " 1>&2 -# echo " --maxiterate # : Maximum number of iterative refinement, default: $defaultiterate " 1>&2 -# if [ $defaultfft -eq 1 ]; then -# echo " --fft or --nofft: FFT is enabled or disabled, default: enabled" 1>&2 -# else -# echo " --fft or --nofft: FFT is enabled or disabled, default: disabled" 1>&2 -# fi -# echo " --memsave: Memory saving mode" 1>&2 -# echo " (for long genomic sequences), default: off" 1>&2 -# echo " --clustalout : Output: clustal format, default: fasta" 1>&2 -# echo " --reorder : Outorder: aligned, default: input order" 1>&2 -# echo " --quiet : Do not report progress" 1>&2 -# echo "-----------------------------------------------------------------------------" 1>&2 - exit 1; - fi - if [ $sw -eq 1 ]; then - swopt=" -A " - else - swopt=" " - fi - - if [ $distance = "fasta" -o $partdist = "fasta" ]; then - if [ ! "$FASTA_4_MAFFT" ]; then - FASTA_4_MAFFT=`which fasta34` - fi - - if [ ! -x "$FASTA_4_MAFFT" ]; then - echo "" 1>&2 - echo "== Install FASTA ========================================================" 1>&2 - echo "This option requires the fasta34 program (FASTA version x.xx or higher)" 1>&2 - echo "installed in your PATH. If you have the fasta34 program but have renamed" 1>&2 - echo "(like /usr/local/bin/myfasta), set the FASTA_4_MAFFT environment variable" 1>&2 - echo "to point your fasta34 (like setenv FASTA_4_MAFFT /usr/local/bin/myfasta)." 1>&2 - echo "=========================================================================" 1>&2 - echo "" 1>&2 - exit 1 - fi - fi - if [ $distance = "last" -o $distance = "lastmulti" ]; then - if [ ! -x "$prefix/lastal" -o ! -x "$prefix/lastdb" ]; then - echo "" 1>&2 - echo "== Install LAST ============================================================" 1>&2 - echo "LAST (Kielbasa, Wan, Sato, Horton, Frith 2011 Genome Res. 21:487) is required." 1>&2 - echo "http://last.cbrc.jp/" 1>&2 - echo "http://mafft.cbrc.jp/alignment/software/xxxxxxx.html " 1>&2 - echo "============================================================================" 1>&2 - echo "" 1>&2 - exit 1 - fi - fi - if [ $distance = "lara" -o $distance = "slara" ]; then - if [ ! -x "$prefix/mafft_lara" ]; then - echo "" 1>&2 - echo "== Install LaRA =========================================================" 1>&2 - echo "This option requires LaRA (Bauer et al. http://www.planet-lisa.net/)." 1>&2 - echo "The executable have to be renamed to 'mafft_lara' and installed into " 1>&2 - echo "the $prefix directory. " 1>&2 - echo "A configuration file of LaRA also have to be given" 1>&2 - echo "mafft-xinsi --larapair --laraparams parameter_file" 1>&2 - echo "mafft-xinsi --slarapair --laraparams parameter_file" 1>&2 - echo "=========================================================================" 1>&2 - echo "" 1>&2 - exit 1 - fi - if [ ! -s "$laraparams" ]; then - echo "" 1>&2 - echo "== Configure LaRA =======================================================" 1>&2 - echo "A configuration file of LaRA have to be given" 1>&2 - echo "mafft-xinsi --larapair --laraparams parameter_file" 1>&2 - echo "mafft-xinsi --slarapair --laraparams parameter_file" 1>&2 - echo "=========================================================================" 1>&2 - echo "" 1>&2 - exit 1 - fi - fi - if [ $distance = "foldalignlocal" -o $distance = "foldalignglobal" ]; then - if [ ! -x "$prefix/foldalign210" ]; then - echo "" 1>&2 - echo "== Install FOLDALIGN ====================================================" 1>&2 - echo "This option requires FOLDALIGN (Havgaard et al. http://foldalign.ku.dk/)." 1>&2 - echo "The executable have to be renamed to 'foldalign210' and installed into " 1>&2 - echo "the $prefix directory. " 1>&2 - echo "=========================================================================" 1>&2 - echo "" 1>&2 - exit 1 - fi - fi - if [ $distance = "scarna" -o $mccaskill -eq 1 ]; then - if [ ! -x "$prefix/mxscarnamod" ]; then - echo "" 1>&2 - echo "== Install MXSCARNA ======================================================" 1>&2 - echo "MXSCARNA (Tabei et al. BMC Bioinformatics 2008 9:33) is required." 1>&2 - echo "Please 'make' at the 'extensions' directory of the MAFFT source package," 1>&2 - echo "which contains the modified version of MXSCARNA." 1>&2 - echo "http://mafft.cbrc.jp/alignment/software/source.html " 1>&2 - echo "==========================================================================" 1>&2 - echo "" 1>&2 - exit 1 - fi - fi - if [ $distance = "dafs" -o $dafs -eq 1 ]; then - if [ ! -x "$prefix/dafs" ]; then - echo "" 1>&2 - echo "== Install DAFS===========================================================" 1>&2 - echo "DAFS (Sato et al. Journal 2012 issue:page) is required." 1>&2 - echo "http://www.ncrna.org/ " 1>&2 - echo "==========================================================================" 1>&2 - echo "" 1>&2 - exit 1 - fi - fi - if [ $contrafold -eq 1 ]; then - if [ ! -x "$prefix/contrafold" ]; then - echo "" 1>&2 - echo "== Install CONTRAfold ===================================================" 1>&2 - echo "This option requires CONTRAfold" 1>&2 - echo "(Do et al. http://contra.stanford.edu/contrafold/)." 1>&2 - echo "The executable 'contrafold' have to be installed into " 1>&2 - echo "the $prefix directory. " 1>&2 - echo "=========================================================================" 1>&2 - echo "" 1>&2 - exit 1 - fi - fi - -#old -# if [ $treeout -eq 1 ]; then -# parttreeoutopt="-t" -# if [ $cycle -eq 0 ]; then -# treeoutopt="-t -T" -# groupsize=1 -# iterate=0 -# if [ $distance = "global" -o $distance = "local" -o $distance = "localgenaf" -o $distance = "globalgenaf" ]; then -# distance="distonly" -# fi -# else -# treeoutopt="-t" -# fi -# else -# parttreeoutopt=" " -# if [ $cycle -eq 0 ]; then -# treeoutopt="-t -T" -# iterate=0 -# if [ $distance = "global" -o $distance = "local" -o $distance = "localgenaf" -o $distance = "globalgenaf" ]; then -# distance="distonly" -# fi -# else -# treeoutopt=" " -# fi -# fi - -#new - if [ $cycle -eq 0 ]; then - if [ $nodeout -eq 1 ]; then - treeoutopt="-^ -T" - else - treeoutopt="-t -T" - fi - iterate=0 - weighti="0.0" # 2016Jul31, tbfast.c kara idou -# if [ $distance = "global" -o $distance = "local" -o $distance = "localgenaf" -o $distance = "globalgenaf" ]; then # 2012/04, localpair --> local alignment distance -# if [ $distance = "global" ]; then -# distance="distonly" -# fi - if [ $treeout -eq 1 ]; then - parttreeoutopt="-t" - groupsize=1 - else - parttreeoutopt=" " - fi - if [ $distout -eq 1 ]; then - distoutopt="-y -T" - if [ $treeout -eq 0 ]; then - treeoutopt="" - fi - fi - else - if [ $nodeout -eq 1 ]; then - if [ $iterate -gt 0 ]; then - echo "The --nodeout option supports only progressive method (--maxiterate 0) for now." 1>&2 - exit 1 - fi - parttreeoutopt="-t" - treeoutopt="-^" - elif [ $treeout -eq 1 ]; then - parttreeoutopt="-t" - treeoutopt="-t" - else - parttreeoutopt=" " - treeoutopt=" " - fi - if [ $distout -eq 1 ]; then - distoutopt="-y" - fi - fi -# - - formatcheck=`grep -c '^[[:blank:]]\+>' "$TMPFILE/infile" | head -1 ` - if [ $formatcheck -gt 0 ]; then - echo "The first character of a description line must be " 1>&2 - echo "the greater-than (>) symbol, not a blank." 1>&2 - echo "Please check the format around the following line(s):" 1>&2 - grep -n '^[[:blank:]]\+>' "$TMPFILE/infile" 1>&2 - exit 1 - fi - - nseq=`grep -c '^[>|=]' "$TMPFILE/infile" | head -1 ` - if [ $nseq -eq 2 ]; then - cycle=1 - fi - if [ $cycle -gt 3 ]; then - cycle=3 - fi - - if [ $nseq -gt 60000 -a $iterate -gt 1 ]; then # 2014/Oct/22, test - echo "Too many sequences to perform iterative refinement!" 1>&2 - echo "Please use a progressive method." 1>&2 - exit 1 - fi - if [ $distance = "lastmulti" -o $distance = "multi" ]; then - if [ $fragment -eq 0 ]; then - echo 'Specify --addfragments too' 1>&2 - exit 1 - fi - fi - - if [ $fragment -ne 0 ]; then - if [ $pairspecified -eq 0 ]; then - distance="multi" - fi - if [ $distance != "multi" -a $distance != "hybrid" -a $distance != "lastmulti" -a $distance != "local" -a $distance != "last" -a $distance != "ktuples" -a $distance != "ktuplesmulti" ]; then - echo 'Specify --multipair, --lastmultipair, --lastpair, --localpair, --6merpair, --6mermultipair or --hybridpair' 1>&2 - exit 1 - fi - fi - - if [ "$memopt" = " -M -B " -a "$distance" != "ktuples" ]; then - echo "Impossible" 1>&2 - exit 1 - fi - - if [ $distance = "parttree" ]; then - if [ "$mergetable" != "/dev/null" ]; then - echo "The combination of (dp)parttree and merge is Impossible. " 1>&2 - exit 1 - fi - if [ $addfile != "/dev/null" ]; then - echo "The combination of (dp)parttree and add(fragments) is Impossible. " 1>&2 - exit 1 - fi - if [ $seed != "x" -o $seedtable != "x" ]; then - echo "Impossible" 1>&2 - exit 1 - fi - if [ $iterate -gt 1 ]; then - echo "Impossible" 1>&2 - exit 1 - fi - if [ $outorder = "aligned" ]; then - outorder="input" - fi - outorder="input" # partorder ga kiku - if [ $partdist = "localalign" ]; then - splitopt=" -U " # -U -l -> fast - cycle=1 - elif [ $partdist = "fasta" ]; then - splitopt=" -S " - cycle=1 - else - splitopt=" " - fi - fi - - - if [ \( $distance = "ktuples" -o $distance = "ktuplesmulti" \) -a \( $seed = "x" -a $seedtable = "x" -a $ownlist = "/dev/null" -a $pdblist = "/dev/null" -a $enrichstr -eq 0 -a $newdash -eq 0 \) ]; then - localparam="" - weighti="0.0" - elif [ \( $distance = "ktuples" -o $distance = "ktuplesmulti" \) -a \( $seed != "x" -o $seedtable != "x" -o $ownlist != "/dev/null" -o $pdblist != "/dev/null" -o $enrichstr -eq 1 -o $newdash -eq 1 \) ]; then - if [ $cycle -lt 2 ]; then - cycle=2 # disttbfast ha seed hi-taiou # chuui 2014Aug21 - fi - if [ $iterate -lt 2 ]; then - echo "############################################################################" 1>&2 - echo "# Warning:" 1>&2 - echo "# Progressive alignment method is incompatible with the --seed option." 1>&2 - echo "# Automatically switched to the iterative refinement method." 1>&2 - echo "# " 1>&2 - echo "# Also consider using the '--add' option, which is compatible with" 1>&2 - echo "# the progressive method and FASTER than the '--seed' option." 1>&2 - echo "# Usage is:" 1>&2 - echo "# % mafft --add newSequences existingAlignment > output" 1>&2 - echo "############################################################################" 1>&2 - iterate=2 - fi - localparam="-l "$weighti - elif [ $distance = "parttree" ]; then - localparam="" - weighti="0.0" - if [ $groupsize -gt -1 ]; then - cycle=1 - fi - else -# localparam="-B -l "$weighti # weighti=0 demo bunkatsu nashi - localparam="-l "$weighti # -B (bunkatsunashi) ha dvtditr.c de taiou (17/Jan/15) - if [ $cycle -gt 1 ]; then # 09/01/08 - cycle=1 - fi - fi - - - if [ $distance = "localgenaf" -o $distance = "globalgenaf" ]; then - aof="0.000" - if [ $oldgenafparam -ne 1 ]; then - laof="0.0" - lexp="0.0" -# LEXP="0.0" # default = 0.0 - usenaivepairscore="-Z" - fi - fi - - -# if [ $nseq -gt 5000 ]; then -# fft=0 -# fi - if [ $forcefft -eq 1 ]; then - param_fft=" -G " - fft=1 - elif [ $fft -eq 1 ]; then - param_fft=" -F " - else - param_fft=" " - fi - - if [ $seed != "x" -a $seedtable != "x" ]; then - echo 'Use either one of seedtable and seed. Not both.' 1>&2 - exit 1 - fi - if [ $f2clext = "-E" -a $anysymbol -gt 0 ]; then - echo '' 1>&2 - echo 'The combination of --text and ( --anysymbol or --preservecase ) is impossible.' 1>&2 - echo '' 1>&2 - exit 1 - fi - -# if [ $f2clext = "-E" -a $scorematrix != "/dev/null" ]; then -# echo '' 1>&2 -# echo 'At present, the combination of --text and (--aamatrix) is impossible.' 1>&2 -# echo '' 1>&2 -# exit 1 -# fi - - memsavetree=0 - if [ $treeext != "none" ]; then - if [ $distance == "ktuples" ]; then - treein=1 - treeinopt=" -U " - if [ $treeext == "randomchain" ]; then - echo "shuffle $randomseed" > "$TMPFILE/_guidetree" - cycle=1 # disttbfast.c dem shitei - elif [ $treeext == "pileup" ]; then - echo "pileup" > "$TMPFILE/_guidetree" - cycle=1 # disttbfast. shitei - elif [ $treeext == "memsavetree" ]; then - echo "very compact" > "$TMPFILE/_guidetree" - memsavetree=1 - elif [ $treeext == "memsavetreex" ]; then - echo "compact " "$initialramusage" > "$TMPFILE/_guidetree" - memsavetree=1 - elif [ $treeext == "stepadd" ]; then - echo "stepadd" > "$TMPFILE/_guidetree" - memsavetree=1 - elif [ $treeext == "youngestlinkage" ]; then - echo "youngestlinkage" > "$TMPFILE/_guidetree" - memsavetree=1 - else - echo "error in mafft.tmpl" - exit - fi - else # globalpair, localpair, genafpair, oldgenafpair -# treein, treeinopt ha kimaranai - if [ $treeext == "memsavetree" -o $treeext == "stepadd" ]; then - memsavetree=1 - else - echo "With globalpair, localpair or genafpair," 1>>"$progressfile" - echo "Use --large, --minimumlinkage, --averagelinkage or --mixedlinkage." 1>>"$progressfile" - echo "--$treeext is supported only with --6merpair." 1>>"$progressfile" - echo '' 1>>"$progressfile" - exit - fi - fi - if [ $iterate -gt 0 ]; then - echo 'Iterative refinment is not supported for --large or --'$treeext 1>>"$progressfile" - echo '' 1>>"$progressfile" - exit 1 - fi - if [ $fragment -ne 0 ]; then - echo '--addfragments, --addfull or --addlong is not yet supported for --large or --'$treeext 1>>"$progressfile" - echo "Use --add newsequences --$treeext" 1>>"$progressfile" - echo "Or, --addfragments (long, full) newsequences, without --"$treeext 1>>"$progressfile" - echo '' 1>>"$progressfile" - exit 1 - fi - if [ "$mergetable" != "/dev/null" ]; then # 2018/Mar/2 - echo '--merge is not yet supported for --large or --'$treeext 1>>"$progressfile" - echo "Use --merge without --"$treeext 1>>"$progressfile" - echo '' 1>>"$progressfile" - exit 1 - fi - fi - - - - if [ $nadd -gt "0" ]; then - if [ $fragment -eq "1" ]; then - addarg="$addarg0 $nadd -g -0.01" - addsinglearg="" - cycle=1 # chuui 2014Aug25 - iterate=0 - elif [ $fragment -eq "-1" ]; then - addarg="$addarg0 $nadd" - addsinglearg="-V" # allowlongadds, 2014/04/02 - cycle=1 # chuui 2014Aug25 - iterate=0 - elif [ $fragment -eq "-2" ]; then - addarg="$addarg0 $nadd" - addsinglearg="-V" # allowlongadds + smoothing - add2ndhalfarg=$add2ndhalfarg" -p " - cycle=1 # chuui 2014Aug25 - usenaivepairscore="-Z" # 2015Jun01 - laof=0.0 # 2015Jun01 - lexp=0.0 # 2015Jun01 - iterate=0 - elif [ $fragment -eq "-3" ]; then - addarg="$addarg0 $nadd" - addsinglearg="-x" # add to top, 2021/12/31 - cycle=1 # chuui 2014Aug25 - iterate=0 - elif [ $fragment -eq "-4" ]; then - addarg="$addarg0 $nadd" - addsinglearg="-s" # add to root, 2023/2/11 - cycle=1 # chuui 2014Aug25 - iterate=0 - else - addarg="$addarg0 $nadd" - addsinglearg="" -# iterate=1 # iterate ha shitei dori - bunkatsuopt=" -B " # fftnsi demo bunktasu shinai - if [ "$add2ndhalfarg" != " " ]; then - if [ $auto -eq 1 -o $iterate -gt 0 ]; then -# echo '' 1>>"$progressfile" -# echo 'The --keeplength and --mapout options are not supported' 1>>"$progressfile" -# echo 'with the --auto or --maxiterate >0 options.' 1>>"$progressfile" -# echo 'Use the --maxiterate 0 option (= progressive method).' 1>>"$progressfile" -# echo '' 1>>"$progressfile" -# exit 1 - iterate=0 - fi - fi - fi - - -# cycle=1 # chuui 2014Aug19 -# iterate=0 -# treealg=" -q " ## 2012/01/24 ## removed 2012/02/06 - else - if [ "$add2ndhalfarg" != " " ]; then - echo '' 1>>"$progressfile" - echo 'The --keeplength and --mapout options are supported' 1>>"$progressfile" - echo 'only with --add, --addfragments or --addlong.' 1>>"$progressfile" - echo '' 1>>"$progressfile" - exit 1 - fi - fi - - if [ "$codonposfile" != "/dev/null" -o "$codonscorefile" != "/dev/null" ]; then - if [ $nadd -eq "0" -o $fragment -eq "0" ]; then - echo '' 1>>"$progressfile" - echo "'--codonpos' and '--codonscore' options are supported only with the '--6merpair --addfragments' option." 1>>"$progressfile" - echo '' 1>>"$progressfile" - exit 1 - fi - if [ $distance != "ktuples" ]; then # ato de taiou - echo '' 1>>"$progressfile" - echo "'--codonpos' and '--codonscore' options are supported only with the '--6merpair --addfragments' option, at this point." 1>>"$progressfile" - echo '' 1>>"$progressfile" - exit 1 - fi - fi - - - if [ -z "$localparam" -a $fragment -eq 0 -a $distance != "parttree" ]; then -# echo "use disttbfast" -# echo cycle = $cycle - cycletbfast=1 # tbfast wo jikkou shinai - cycledisttbfast=$cycle # disttbfast ni -E cycle wo watasu - if [ $cycledisttbfast -eq 0 ]; then # --treeout de tsukau - cycledisttbfast=1 - fi - else -# echo "use tbfast" -# echo cycle = $cycle - cycletbfast=$cycle # 1 ijou nara jikkou - cycledisttbfast=1 # disttbfast ha ikkai dake - fi - -# echo localparam= -# echo $localparam -# echo cycletbfast= -# echo $cycletbfast -# echo cycledisttbfast= -# echo $cycledisttbfast - -#exit - - if [ $adjustdirection -gt 0 -a $seed != "x" ]; then - echo '' 1>&2 - echo 'The combination of --adjustdirection(accurately) and --seed is not supported.' 1>&2 - echo '' 1>&2 - exit 1 - fi - - - if [ $mccaskill -eq 1 -o $dafs -eq 1 -o $rnaalifold -eq 1 -o $contrafold -eq 1 ]; then - if [ $distance = "ktuples" ]; then - echo 'Not supported.' 1>&2 - echo 'Please add --globalpair, --localpair, --scarnapair, --dafspair' 1>&2 - echo '--larapair, --slarapair, --foldalignlocalpair or --foldalignglobalpair' 1>&2 - exit 1 - fi - if [ $f2clext = "-E" ]; then - echo '' 1>&2 - echo 'For RNA alignment, the --text mode is impossible.' 1>&2 - echo '' 1>&2 - exit 1 - fi - fi - -# cycle ga atode henkou sareru node koko de strategy no namae wo kimeru. -# kokokara - if [ $treeext = "pileup" ]; then - strategy="Pileup-" - elif [ $treeext = "randomchain" ]; then - strategy="Randomchain-" - elif [ $mccaskill -eq 1 -o $dafs -eq 1 -o $rnaalifold -eq 1 -o $contrafold -eq 1 ]; then - if [ $distance = "scarna" -o $distance = "dafs" -o $distance = "lara" -o $distance = "slara" -o $distance = "foldalignlocal" -o $distance = "foldalignglobal" ]; then - strategy="X-" - elif [ $distance = "global" -o $distance = "local" -o $distance = "localgenaf" -o "globalgenaf" ]; then - strategy="Q-" - fi - elif [ $distance = "fasta" -a $sw -eq 0 ]; then - strategy="F-" - elif [ $distance = "fasta" -a $sw -eq 1 ]; then - strategy="H-" - elif [ $distance = "blast" ]; then - strategy="B-" - elif [ $distance = "global" -o $distance = "distonly" ]; then - strategy="G-" - elif [ $distance = "local" ]; then - strategy="L-" - elif [ $distance = "last" ]; then - strategy="Last-" - elif [ $distance = "hybrid" ]; then - strategy="Hybrid-" - elif [ $distance = "multi" ]; then - strategy="Multi-" - elif [ $distance = "lastmulti" ]; then - strategy="LastMulti-" - elif [ $distance = "localgenaf" ]; then - strategy="E-" - elif [ $distance = "globalgenaf" ]; then - strategy="K-" - elif [ $fft -eq 1 ]; then - strategy="FFT-" - else - strategy="NW-" - fi - if [ $memsavetree -eq 1 ]; then - strategy=$strategy"large-" - fi -# if [ `echo "$weighti>0.0" | bc` -gt 0 ]; then - if [ `awk "BEGIN {print(0.0+\"$weighti\">0.0)}"` -gt 0 ]; then - strategy=$strategy"I" - fi - strategy=$strategy"NS-" - if [ $iterate -gt 0 ]; then - strategy=$strategy"i" - elif [ $distance = "parttree" ]; then - if [ $partdist = "fasta" ]; then - strategy=$strategy"FastaPartTree-"$cycle - elif [ $partdist = "localalign" ]; then - strategy=$strategy"DPPartTree-"$cycle - else - strategy=$strategy"PartTree-"$cycle - fi - elif [ $fragment -eq 1 ]; then - strategy=$strategy"fragment" - elif [ $fragment -eq -1 ]; then - strategy=$strategy"full" - elif [ $fragment -eq -2 ]; then - strategy=$strategy"long" - elif [ $fragment -eq -3 ]; then - strategy=$strategy"top" - else - strategy=$strategy$cycle - fi - - explanation='?' - performance='Not tested.' - if [ $strategy = "F-INS-i" ]; then - explanation='Iterative refinement method (<'$iterate') with LOCAL pairwise alignment information' - performance='Most accurate, but very slow' - elif [ $strategy = "L-INS-i" ]; then - explanation='Iterative refinement method (<'$iterate') with LOCAL pairwise alignment information' - performance='Probably most accurate, very slow' - elif [ $strategy = "E-INS-i" ]; then - explanation='Iterative refinement method (<'$iterate') with LOCAL pairwise alignment with generalized affine gap costs (Altschul 1998)' - performance='Suitable for sequences with long unalignable regions, very slow' - elif [ $strategy = "G-INS-i" ]; then - explanation='Iterative refinement method (<'$iterate') with GLOBAL pairwise alignment information' - performance='Suitable for sequences of similar lengths, very slow' - elif [ $strategy = "X-INS-i" ]; then - explanation='RNA secondary structure information is taken into account.' - performance='For short RNA sequences only, extremely slow' - elif [ $strategy = "F-INS-1" ]; then - explanation='Progressive method incorporating LOCAL pairwise alignment information' - elif [ $strategy = "L-INS-1" ]; then - explanation='Progressive method incorporating LOCAL pairwise alignment information' - elif [ $strategy = "G-INS-1" ]; then - explanation='Progressive method incorporating GLOBAL pairwise alignment information' - elif [ $strategy = "FFT-NS-i" -o $strategy = "NW-NS-i" ]; then - explanation='Iterative refinement method (max. '$iterate' iterations)' - if [ $iterate -gt 2 ]; then - performance='Accurate but slow' - else - performance='Standard' - fi - elif [ $strategy = "FFT-NS-2" -o $strategy = "NW-NS-2" ]; then - explanation='Progressive method (guide trees were built '$cycle' times.)' - performance='Fast but rough' - elif [ $strategy = "FFT-NS-1" -o $strategy = "NW-NS-1" ]; then - explanation='Progressive method (rough guide tree was used.)' - performance='Very fast but very rough' - fi - - if [ $outputformat = "clustal" -a $outorder = "aligned" ]; then - outputopt=" -c $strategy -r $TMPFILE/order $f2clext " - elif [ $outputformat = "clustal" -a $outorder = "input" ]; then - outputopt=" -c $strategy $f2clext " - elif [ $outputformat = "phylip" -a $outorder = "aligned" ]; then - outputopt=" -y -r $TMPFILE/order " - elif [ $outputformat = "phylip" -a $outorder = "input" ]; then - outputopt=" -y " - elif [ $outputformat = "pir" -a $outorder = "aligned" ]; then - outputopt=" -f -l $linelength -r $TMPFILE/order " - else - outputopt="-f -l $linelength" - fi - - if [ $newdash_originalsequenceonly -eq 1 ]; then - outputopt="$outputopt -d " - fi -# kokomade - - - - pushd "$TMPFILE" > /dev/null - - cat /dev/null > pre - -# echo "nseq = " $nseq 1>>"$progressfile" -# echo "distance = " $distance 1>>"$progressfile" -# echo "iterate = " $iterate 1>>"$progressfile" -# echo "cycle = " $cycle 1>>"$progressfile" - - - if [ $anysymbol -eq 1 ]; then - mv infile orig - "$prefix/replaceu" $seqtype -i orig > infile 2>>"$progressfile" || exit 1 - fi - - if [ $mergetable != "/dev/null" ]; then - if [ $nadd -gt "0" ]; then - echo "Impossible" 1>&2 - exit 1 - fi -# if [ $seed != "x" -o $seedtable != "x" ]; then -# echo "This version does not support the combination of merge and seed." 1>&2 -# exit 1 -# fi -# iterate=0 # 2013/04/16 - mergearg="-H $seedoffset" - fi - - if [ $adjustdirection -gt 0 ]; then - if [ $fragment -ne 0 ]; then - fragarg="-F" # - else - fragarg="-F" # 2014/02/06, do not consider other additional sequences, even in the case of --add - fi - if [ $adjustdirection -eq 1 ]; then - "$prefix/makedirectionlist" $fragarg -C $numthreads -m -I $nadd -i infile -t 0.00 -r 5000 -o a > _direction 2>>"$progressfile" - elif [ $adjustdirection -eq 2 ]; then - "$prefix/makedirectionlist" $fragarg -C $numthreads -m -I $nadd -i infile -t 0.00 -r 100 -o a -d > _direction 2>>"$progressfile" - fi - "$prefix/setdirection" $mergearg -d _direction -i infile > infiled 2>>"$progressfile" || exit - mv infiled infile - if [ $anysymbol -eq 1 ]; then - "$prefix/setdirection" $mergearg -d _direction -i orig -r > origd 2>>"$progressfile" || exit - mv origd orig - fi - fi - - if [ $seed != "x" -o $seedtable != "x" ]; then - if [ $pdblist != "/dev/null" -o $ownlist != "/dev/null" ]; then - echo "The combination of --seed and (--pdbidlist or --pdbfilelist) is impossible." 1>>"$progressfile" - exit 1 - fi -# if [ $enrich -eq 1 ]; then -# echo "The combination of --seed and (--enrich, --enrichseq or --enrichstr) is impossible at present." 1>>"$progressfile" -# exit 1 -# fi - - if [ $newdash -eq 1 ]; then - echo "The combination of --seed and --dash is impossible at present." 1>>"$progressfile" - exit 1 - fi - fi - - -# if [ $enrich -eq 1 ]; then -# if [ $ownlist != "/dev/null" ]; then -# echo "Warning: Sequence homologs of the structures given with the --pdbfilelist option cannot be collected.\n" 1>>"$progressfile" -# fi -# echo "SEEKQUENCER (http://sysimm.ifrec.osaka-u.ac.jp/seekquencer/) is" 1>>"$progressfile" -# if [ $pdblist != "/dev/null" ]; then -# echo "collecting homoplogs of the input sequences and the structures given with the --pdbidlist option." 1>>"$progressfile" -# perl "$prefix/seekquencer_premafft.pl" $seektarget -run thread -trd 2 -seqd uniref90 -blim 1000 -noin -seqf infile -idf pdblist -out seekout -mod mafftash-split 2>>"seekerr" -# seekres="$?" -# else -# echo "collecting homologs of the input sequences." 1>>"$progressfile" -# perl "$prefix/seekquencer_premafft.pl" $seektarget -run thread -trd 2 -seqd uniref90 -blim 1000 -noin -seqf infile -out seekout -mod mafftash-split 2>>"seekerr" -# seekres="$?" -# fi -# cat seekerr 1>>"$progressfile" -# -# if [ $seekres -ne "0" ]; then -# echo "Error in SEEKQUENCER" 1>>"$progressfile" -# exit 1; -# fi -# echo "Done." 1>>"$progressfile" -# -# if [ $enrichseq -eq 1 ]; then -## cat seekout.seq >> infile -# if [ $anysymbol -eq 1 ]; then -# "$prefix/replaceu" $seqtype -i seekout.seq -o $nseq >> infile -# cat seekout.seq >> orig -# else -# "$prefix/replaceu" $seqtype -i seekout.seq | sed 's/_os_[0-9]*_oe_//' >> infile -# fi -# -# fi -# if [ $enrichstr -eq 1 ]; then -# nseekstr=`wc -l < seekout.str` -# if [ $nseekstr -gt 1 ]; then -# cat seekout.str >> pdblist -# pdblist="tsukaimasu" -# fi -# fi -# fi - - if [ $seed != "x" ]; then - mv infile infile2 - if [ $anysymbol -eq 1 ]; then - mv orig orig2 - cat /dev/null > orig - fi - cat /dev/null > infile - cat /dev/null > hat3.seed - seedoffset=0 -# echo "seednseq="$seednseq -# echo "seedoffset="$seedoffset - set $seednseq >> "$progressfile" -# echo $# - while [ $# -gt 1 ] - do - shift -# echo "num="$# - - if [ $anysymbol -eq 1 ]; then - cat seed$# >> orig - "$prefix/replaceu" $seqtype -i seed$# -o $seedoffset > clean 2>>"$progressfile" || exit 1 - mv clean seed$# - fi - "$prefix/multi2hat3s" -t $nseq -o $seedoffset -i seed$# >> infile 2>>"$progressfile" || exit 1 - cat hat3 >> hat3.seed -# echo "$1" - seedoffset=`expr $seedoffset + $1` -# echo "$1" -# echo "seedoffset="$seedoffset - done; -# echo "seedoffset="$seedoffset - if [ $anysymbol -eq 1 ]; then - "$prefix/replaceu" $seqtype -i orig2 -o $seedoffset >> infile 2>>"$progressfile" || exit 1 # yarinaoshi - cat orig2 >> orig - else - cat infile2 >> infile - fi - elif [ $seedtable != "x" ]; then - cat _seedtablefile > hat3.seed - elif [ $newdash -eq 1 ]; then - seemstobe=`"$prefix/countlen" -i infile | awk '{print $6}'` - if [ $seemstobe = "d" -a "x$seqtype" != "x-P" ]; then - echo "" 1>>"$progressfile" - echo "Error: This data seems to be nucleotide sequences." 1>>"$progressfile" - echo "Add the --amino flag if this is surely protein." 1>>"$progressfile" - echo "" 1>>"$progressfile" - exit 1; - fi - if [ $anysymbol -eq 1 ]; then - mv orig infile # replaceu wo mukouka - fi -# sed 's/-//g' infile > dashin # gap nozoku - awk '{if(/^>/)print; else {gsub( /-/,"" ); print;}}' infile > dashin - - if [ ! -x "$prefix/dash_client" -o ! -x "$prefix/dash_client" ]; then - echo "" 1>&2 - echo "== Install DASH client =====================================================" 1>&2 - echo "To use this feature, uncomment the following line in Makefile" 1>&2 - echo "DASH_CLIENT = dash_client" 1>&2 - echo "and re-compile the source." 1>&2 - echo "Note that it requires the 'Go' compiler." 1>&2 - echo "============================================================================" 1>&2 - echo "" 1>&2 - exit 1 - fi - - echo "Calling DASH (https://sysimm.org/dash/)" 1>>"$progressfile" - "$prefix/dash_client" -url "$dashserver" -i dashin -sequences dashsequences -hat3 hat3.seed 1>>"$progressfile" - dashres="$?" - if [ $dashres -ne "0" ]; then - echo "Error in DASH" 1>>"$progressfile" - echo "To enable this feature, compile with DASH_CLIENT=dash_client. Go compiler is necessary." 1>>"$progressfile" - exit 1; - fi - - if [ $exclude_ho -eq 1 ]; then # amari yokunai - awk 'BEGIN{out=1} !/^>_addedbymaffte_/{if(out) print; out=1} /^>_addedbymaffte_/{out=0}' dashsequences | sed 's/>DASH_/>DASH|/' > ho_excluded - mv ho_excluded dashsequences - fi - - if [ "$mergetable" != "/dev/null" ]; then # 2020/Apr/30 - ndash=`grep -c '>DASH_' dashsequences | head -1` -# echo "ndash = " $ndash - awk "{for( i=1;i<=NF;i++){if(0+\$i==0)break; printf( \"%d \", $ndash+\$i); } print \"\" }" _subalignmentstable > _subalignmentstableshifted - mv _subalignmentstableshifted _subalignmentstable - cp dashsequences dashsequences.bk - awk "BEGIN{nout=0} {if(\$1~/^>/) nout++; if( nout <= $ndash ) print;}" dashsequences > infile2 - cat infile >> infile2 - cp infile2 dashsequences - fi - - sed 's/>DASH_/>DASH|/' dashsequences > renamed - mv renamed dashsequences - echo "Done." 1>>"$progressfile" -# cat hat3.seed - seedoffset=`grep -c '^[>|=]' dashsequences | head -1 ` - echo "# of structures = " 1>>"$progressfile" - echo $seedoffset 1>>"$progressfile" - if [ $anysymbol -eq 1 ]; then - cat dashsequences >> orig - "$prefix/replaceu" $seqtype -i dashsequences -o 0 > clean 2>>"$progressfile" || exit 1 - mv clean infile - -# "$prefix/replaceu" $seqtype -i orig2 -o $seedoffset >> infile 2>>"$progressfile" || exit 1 # yarinaoshi -# cat orig2 >> orig - else - cat dashsequences > infile -# cat infile2 >> infile - fi - else - cat /dev/null > hat3.seed - fi -# cat hat3.seed - - if [ $mccaskill -eq 1 ]; then - "$prefix/mccaskillwrap" -s -C $numthreads -d "$prefix" -i infile > hat4 2>>"$progressfile" || exit 1 - elif [ $dafs -eq 1 ]; then - "$prefix/mccaskillwrap" -G -C $numthreads -d "$prefix" -i infile > hat4 2>>"$progressfile" || exit 1 - elif [ $contrafold -eq 1 ]; then - "$prefix/contrafoldwrap" -d "$prefix" -i infile > hat4 2>>"$progressfile" || exit 1 - fi - if [ $distance = "fasta" ]; then - "$prefix/dndfast7" $swopt < infile > /dev/null 2>>"$progressfile" || exit 1 - cat hat3.seed hat3 > hatx - mv hatx hat3 - "$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1 - elif [ $distance = "blast" ]; then - "$prefix/dndblast" < infile > /dev/null 2>>"$progressfile" || exit 1 - cat hat3.seed hat3 > hatx - mv hatx hat3 - "$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1 - elif [ $distance = "foldalignlocal" ]; then - "$prefix/pairlocalalign" -C $numthreads $seqtype $foldalignopt $model -g $lexp -f $lgop -Q $spfactor -h $laof -H -d "$prefix" < infile > /dev/null 2>>"$progressfile" || exit 1 - cat hat3.seed hat3 > hatx - mv hatx hat3 - "$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1 - elif [ $distance = "foldalignglobal" ]; then - "$prefix/pairlocalalign" -C $numthreads $seqtype $foldalignopt $model -g $pgexp -f $pggop -Q $spfactor -h $pgaof -H -o -global -d "$prefix" < infile > /dev/null 2>>"$progressfile" || exit 1 - cat hat3.seed hat3 > hatx - mv hatx hat3 - "$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1 - elif [ $distance = "slara" ]; then - "$prefix/pairlocalalign" -C $numthreads -p $laraparams $seqtype $model -f $lgop -Q $spfactor -T -d "$prefix" < infile > /dev/null 2>>"$progressfile" || exit 1 - cat hat3.seed hat3 > hatx - mv hatx hat3 - "$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1 - elif [ $distance = "lara" ]; then - "$prefix/pairlocalalign" -C $numthreads -p $laraparams $seqtype $model -f $lgop -Q $spfactor -B -d "$prefix" < infile > /dev/null 2>>"$progressfile" || exit 1 - cat hat3.seed hat3 > hatx - mv hatx hat3 - "$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1 - elif [ $distance = "scarna" ]; then -# "$prefix/pairlocalalign" -C $numthreads $seqtype $model -f $pggop -Q $spfactor -s -d "$prefix" < infile > /dev/null 2>>"$progressfile" || exit 1 -# cat hat3.seed hat3 > hatx -# mv hatx hat3 -# "$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1 - "$prefix/tbfast" _ -C $numthreads $seqtype $model -f $pggop -Q $spfactor -s -d "$prefix" _ -+ $iterate -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1 - elif [ $distance = "dafs" ]; then - "$prefix/pairlocalalign" -C $numthreads $seqtype $model -f $pggop -Q $spfactor -G -d "$prefix" < infile > /dev/null 2>>"$progressfile" || exit 1 - cat hat3.seed hat3 > hatx - mv hatx hat3 - "$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1 - elif [ $distance = "global" -a $memsavetree -eq 1 ]; then - if [ "$mpiscript" != "/dev/null" ]; then - sh $mpiscript "$prefix/nodepair_mpi" $lhlimit -u $unalignlevel $localparam $seqtype $model -g $pgexp -f $pggop -Q $spfactor -h $pgaof -A $usenaivepairscore $focusarg $treeinopt $treeoutopt -i infile > /dev/null 2>>"$progressfile" || exit 1 - else - "$prefix/nodepair" $lhlimit -u $unalignlevel $localparam -C $numthreads $seqtype $model -g $pgexp -f $pggop -Q $spfactor -h $pgaof -A $usenaivepairscore $focusarg $treeinopt $treeoutopt -i infile > /dev/null 2>>"$progressfile" || exit 1 - fi - echo 'nodepair' > _guidetree - "$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt -U $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg $focusarg < infile > /dev/null 2>>"$progressfile" || exit 1 - elif [ $distance = "local" -a $memsavetree -eq 1 ]; then - if [ "$mpiscript" != "/dev/null" ]; then - sh $mpiscript "$prefix/nodepair_mpi" $lhlimit -u $unalignlevel $localparam $seqtype $model -g $lexp -f $lgop -Q $spfactor -h $laof -L $usenaivepairscore $focusarg $treeinopt $treeoutopt -i infile > /dev/null 2>>"$progressfile" || exit 1 - else - "$prefix/nodepair" $lhlimit -u $unalignlevel $localparam -C $numthreads $seqtype $model -g $lexp -f $lgop -Q $spfactor -h $laof -L $usenaivepairscore $focusarg $treeinopt $treeoutopt -i infile > /dev/null 2>>"$progressfile" || exit 1 - fi - - echo 'nodepair' > _guidetree - "$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt -U $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg $focusarg < infile > /dev/null 2>>"$progressfile" || exit 1 - elif [ $distance = "localgenaf" -a $memsavetree -eq 1 ]; then - "$prefix/nodepair" $lhlimit -u $unalignlevel $localparam -C $numthreads $seqtype $model -g $lexp -f $lgop -Q $spfactor -h $laof -O $LGOP -E $LEXP -N $usenaivepairscore $focusarg $treeinopt $treeoutopt -i infile > /dev/null 2>>"$progressfile" || exit 1 - echo 'nodepair' > _guidetree - "$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt -U $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg $focusarg < infile > /dev/null 2>>"$progressfile" || exit 1 - elif [ $distance = "global" -a $memsavetree -eq 0 ]; then - "$prefix/tbfast" _ -u $unalignlevel $localparam -C $numthreads $seqtype $model -g $pgexp -f $pggop -Q $spfactor -h $pgaof -A $usenaivepairscore $focusarg _ -+ $iterate -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg $focusarg < infile > /dev/null 2>>"$progressfile" || exit 1 - - elif [ $distance = "local" -a $memsavetree -eq 0 ]; then - if [ $fragment -ne 0 ]; then - "$prefix/pairlocalalign" $localparam $addarg -C $numthreads $seqtype $model -g $lexp -f $lgop -Q $spfactor -h $laof -L $usenaivepairscore < infile > /dev/null 2>>"$progressfile" || exit 1 - cat hat3.seed hat3 > hatx - mv hatx hat3 - "$prefix/addsingle" $codonposopt $codonscoreopt -Q 100 $legacygapopt -O $outnum $addsinglearg $addarg $add2ndhalfarg -C $numthreads $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h $aof $param_fft $localparam $algopt $treealg < infile > /dev/null 2>>"$progressfile" || exit 1 - else - "$prefix/tbfast" _ -u $unalignlevel $localparam -C $numthreads $seqtype $model -g $lexp -f $lgop -Q $spfactor -h $laof -L $usenaivepairscore $focusarg _ -+ $iterate -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg $focusarg < infile > /dev/null 2>>"$progressfile" || exit 1 - fi - elif [ $distance = "globalgenaf" ]; then - "$prefix/pairlocalalign" -u $unalignlevel $localparam -C $numthreads $seqtype $model -g $pgexp -f $pggop -Q $spfactor -h $pgaof -O $GGOP -E $GEXP -K $usenaivepairscore < infile > /dev/null 2>>"$progressfile" || exit 1 - cat hat3.seed hat3 > hatx - mv hatx hat3 - "$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1 - elif [ $distance = "localgenaf" -a $memsavetree -eq 0 ]; then - "$prefix/tbfast" _ -u $unalignlevel $localparam -C $numthreads $seqtype $model -g $lexp -f $lgop -Q $spfactor -h $laof -O $LGOP -E $LEXP -N $usenaivepairscore $focusarg _ -+ $iterate -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg $focusarg < infile > /dev/null 2>>"$progressfile" || exit 1 - elif [ $distance = "last" ]; then - if [ $fragment -ne 0 ]; then - "$prefix/pairlocalalign" $addarg -C $numthreads $seqtype $model -e $last_e -w $last_m -g $lexp -f $lgop -Q $spfactor -h $laof -R $last_subopt $last_once -d "$prefix" < infile > /dev/null 2>>"$progressfile" || exit 1 - cat hat3.seed hat3 > hatx - mv hatx hat3 - "$prefix/addsingle" $codonposopt $codonscoreopt -Q 100 $legacygapopt -O $outnum $addsinglearg $addarg $add2ndhalfarg -C $numthreads $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h $aof $param_fft $localparam $algopt $treealg < infile > /dev/null 2>>"$progressfile" || exit 1 - else - "$prefix/pairlocalalign" -C $numthreads $seqtype $model -e $last_e -w $last_m -g $lexp -f $lgop -Q $spfactor -h $laof -R $last_subopt $last_once -d "$prefix" < infile > /dev/null 2>>"$progressfile" || exit 1 -# addarg wo watasanai - cat hat3.seed hat3 > hatx - mv hatx hat3 - "$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1 - fi - elif [ $distance = "lastmulti" ]; then - "$prefix/dndpre" $model -M 2 $addarg -C $numthreads $seqtype $model -g $lexp -f $lgop -Q $spfactor -h $laof < infile > /dev/null 2>>"$progressfile" || exit 1 - mv hat2 hat2i - "$prefix/pairlocalalign" $addarg -C $numthreads $seqtype $model -e $last_e -w $last_m -g $lexp -f $lgop -Q $spfactor -h $laof -r $last_subopt $last_once -d "$prefix" < infile > /dev/null 2>>"$progressfile" || exit 1 - cat hat3.seed hat3 > hatx - mv hat2 hat2n - mv hatx hat3 - if [ $fragment -ne 0 ]; then - "$prefix/addsingle" $codonposopt $codonscoreopt -Q 100 $legacygapopt -d -O $outnum $addsinglearg $addarg $add2ndhalfarg -C $numthreads $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h $aof $param_fft $localparam $algopt $treealg < infile > /dev/null 2>>"$progressfile" || exit 1 - else - echo "Impossible" 1>&2 - exit 1 - fi - elif [ $distance = "multi" ]; then - "$prefix/dndpre" $model -M 2 $addarg -C $numthreads $seqtype $model -g $lexp -f $lgop -h $laof $usenaivepairscore < infile > /dev/null 2>>"$progressfile" || exit 1 - mv hat2 hat2i - "$prefix/pairlocalalign" $localparam $addarg -C $numthreads $seqtype $model -g $lexp -f $lgop -Q $spfactor -h $laof -Y $usenaivepairscore < infile > /dev/null 2>>"$progressfile" || exit 1 - cat hat3.seed hat3 > hatx - mv hat2 hat2n - mv hatx hat3 - if [ $fragment -ne 0 ]; then - "$prefix/addsingle" $codonposopt $codonscoreopt -Q 100 $legacygapopt -d -O $outnum $addsinglearg $addarg $add2ndhalfarg -C $numthreads $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h $aof $param_fft $localparam $algopt $treealg < infile > /dev/null 2>>"$progressfile" || exit 1 - else - echo "Impossible" 1>&2 - exit 1 - fi - elif [ $distance = "hybrid" ]; then - "$prefix/pairlocalalign" $addarg -C $numthreads $seqtype $model -g $lexp -f $lgop -Q $spfactor -h $laof -Y < infile > /dev/null 2>>"$progressfile" || exit 1 - cat hat3.seed hat3 > hatx - mv hatx hat3 - "$prefix/disttbfast" -E 1 -s $unalignlevel $legacygapopt -W $tuplesize $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreads-$numthreadstb $memopt $weightopt $treeinopt $treeoutopt -T -y $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1 - if [ $fragment -ne 0 ]; then - "$prefix/addsingle" $codonposopt $codonscoreopt -Q 100 $legacygapopt -O $outnum $addsinglearg $addarg $add2ndhalfarg -C $numthreads $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h $aof $param_fft $localparam $algopt $treealg < infile > /dev/null 2>>"$progressfile" || exit 1 - else - "$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1 - fi -# elif [ $distance = "distonly" ]; then -# "$prefix/pairlocalalign" -C $numthreads $seqtype $model -g $pgexp -f $pggop -Q $spfactor -h $pgaof -t < infile > /dev/null 2>>"$progressfile" || exit 1 -# "$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1 - elif [ $distance = "parttree" ]; then - "$prefix/splittbfast" $legacygapopt $algopt $splitopt $partorderopt $parttreeoutopt $memopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof -p $partsize -s $groupsize $treealg $outnum -i infile > pre 2>>"$progressfile" || exit 1 - mv hat3.seed hat3 - elif [ $distance = "ktuplesmulti" ]; then -# "$prefix/dndpre" $model -M 1 $addarg -C $numthreads $seqtype $model -g $lexp -f $lgop -h $laof < infile > /dev/null 2>>"$progressfile" || exit 1 -# mv hat2 hat2i -# "$prefix/disttbfast" -E 1 -s $unalignlevel $legacygapopt -W $tuplesize $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreads-$numthreadstb $memopt $weightopt $treeinopt $treeoutopt -T -y $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1 -# mv hat2 hat2n - if [ $fragment -ne 0 ]; then - "$prefix/addsingle" $codonposopt $codonscoreopt -Q 100 $legacygapopt -d -W $tuplesize -O $outnum $addsinglearg $addarg $add2ndhalfarg -C $numthreads $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h $aof $param_fft $localparam $algopt $treealg < infile > /dev/null 2>>"$progressfile" || exit 1 -# "$prefix/addsingle" -Q 100 $legacygapopt -d -O $outnum $addsinglearg $addarg $add2ndhalfarg -C $numthreads $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h $aof $param_fft $localparam $algopt $treealg < infile > /dev/null 2>>"$progressfile" || exit 1 - else - echo "Impossible" 1>&2 - exit 1 - fi - else - if [ $fragment -ne 0 ]; then - "$prefix/addsingle" $codonposopt $codonscoreopt -Q 100 $legacygapopt -W $tuplesize -O $outnum $addsinglearg $addarg $add2ndhalfarg -C $numthreads $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h $aof $param_fft $localparam $algopt $treealg < infile > /dev/null 2>>"$progressfile" || exit 1 - else - "$prefix/disttbfast" -q $npickup -E $cycledisttbfast -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg -W $tuplesize $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreads-$numthreadstb $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -g $gexp -f "-"$gop -Q $spfactor -h $aof $param_fft $algopt $treealg $scoreoutarg $anchoropt -x $maxanchorseparation $oneiterationopt < infile > pre 2>>"$progressfile" || exit 1 - mv hat3.seed hat3 - fi - fi - while [ $cycletbfast -gt 1 ] - do - if [ $distance = "parttree" ]; then - mv pre infile - "$prefix/splittbfast" $legacygapopt -Z $algopt $splitopt $partorderopt $parttreeoutopt $memopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof -p $partsize -s $groupsize $treealg $outnum -i infile > pre 2>>"$progressfile" || exit 1 - else - "$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $termgapopt $outnum -C $numthreadstb $rnaopt $weightopt $treeoutopt $distoutopt $memopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt -J $treealg $scoreoutarg < pre > /dev/null 2>>"$progressfile" || exit 1 -# fragment>0 no baai, nanimoshinai -# seed youchuui!! - fi - cycletbfast=`expr $cycletbfast - 1` - done - if [ $iterate -gt 0 ]; then - if [ $distance = "ktuples" ]; then - "$prefix/dndpre" $seqtype $model -M 2 -C $numthreads < pre > /dev/null 2>>"$progressfile" || exit 1 - fi - "$prefix/dvtditr" -W $minimumweight $bunkatsuopt -E $fixthreshold -s $unalignlevel $legacygapopt $mergearg $outnum -C $numthreadsit -t $randomseed $rnaoptit $memopt $scorecalcopt $localparam -z 50 $seqtype $model -f "-"$gop -Q $spfactor -h $aof -I $iterate $weightopt $treeinopt $algoptit $treealg -p $parallelizationstrategy $scoreoutarg -K $nadd < pre > /dev/null 2>>"$progressfile" || exit 1 - fi - if [ $coreout -eq 1 ]; then - "$prefix/setcore" -w $corewin -i $corethr $coreext < pre > pre2 - mv pre2 pre - elif [ $anysymbol -eq 1 ]; then - "$prefix/restoreu" $add2ndhalfarg -a pre -i orig > restored || exit 1 - mv restored pre - fi - - - - - echo '' 1>>"$progressfile" - if [ $mccaskill -eq 1 ]; then - echo "RNA base pairing probaility was calculated by the McCaskill algorithm (1)" 1>>"$progressfile" - echo "implemented in Vienna RNA package (2) and MXSCARNA (3), and then" 1>>"$progressfile" - echo "incorporated in the iterative alignment process (4)." 1>>"$progressfile" - echo "(1) McCaskill, 1990, Biopolymers 29:1105-1119" 1>>"$progressfile" - echo "(2) Hofacker et al., 2002, J. Mol. Biol. 319:3724-3732" 1>>"$progressfile" - echo "(3) Tabei et al., 2008, BMC Bioinformatics 9:33" 1>>"$progressfile" - echo "(4) Katoh and Toh, 2008, BMC Bioinformatics 9:212" 1>>"$progressfile" - echo "" 1>>"$progressfile" - elif [ $contrafold -eq 1 ]; then - echo "RNA base pairing probaility was calculated by the CONTRAfold algorithm (1)" 1>>"$progressfile" - echo "and then incorporated in the iterative alignment process (4)." 1>>"$progressfile" - echo "(1) Do et al., 2006, Bioinformatics 22:e90-98" 1>>"$progressfile" - echo "(2) Katoh and Toh, 2008, BMC Bioinformatics 9:212" 1>>"$progressfile" - echo "" 1>>"$progressfile" - fi - if [ $pdblist != "/dev/null" -o $ownlist != "/dev/null" ]; then - echo "Input structures are decomposed into structural domains using" 1>>"$progressfile" - echo "Protein Domain Parser (Alexandrov & Shindyalov 2003)." 1>>"$progressfile" - echo "Domain pairs are aligned using the rash function in" 1>>"$progressfile" - echo "the ASH structural alignment package (Standley et al. 2007)." 1>>"$progressfile" - fi - if [ $pdblist != "/dev/null" ]; then - echo "Pre-computed alignments stored in " 1>>"$progressfile" - echo "DASH (http://sysimm.ifrec.osaka-u.ac.jp/dash/) are used. " 1>>"$progressfile" - fi - if [ $distance = "fasta" -o $partdist = "fasta" ]; then - echo "Pairwise alignments were computed by FASTA" 1>>"$progressfile" - echo "(Pearson & Lipman, 1988, PNAS 85:2444-2448)" 1>>"$progressfile" - fi - if [ $distance = "blast" ]; then - echo "Pairwise alignments were computed by BLAST" 1>>"$progressfile" - echo "(Altschul et al., 1997, NAR 25:3389-3402)" 1>>"$progressfile" - fi - if [ $distance = "last" -o $distance = "lastmulti" ]; then - echo "Pairwise alignments were computed by LAST" 1>>"$progressfile" - echo "http://last.cbrc.jp/" 1>>"$progressfile" - echo "Kielbasa, Wan, Sato, Horton, Frith 2011 Genome Res. 21:487" 1>>"$progressfile" - fi - if [ $distance = "scarna" ]; then - echo "Pairwise alignments were computed by MXSCARNA" 1>>"$progressfile" - echo "(Tabei et al., 2008, BMC Bioinformatics 9:33)." 1>>"$progressfile" - fi - if [ $distance = "dafs" ]; then - echo "Pairwise alignments were computed by DAFS" 1>>"$progressfile" - echo "(Sato et al., 2012,,,,)." 1>>"$progressfile" - fi - if [ $distance = "lara" -o $distance = "slara" ]; then - echo "Pairwise alignments were computed by LaRA" 1>>"$progressfile" - echo "(Bauer et al., 2007, BMC Bioinformatics 8:271)." 1>>"$progressfile" - fi - if [ $distance = "foldalignlocal" ]; then - echo "Pairwise alignments were computed by FOLDALIGN (local)" 1>>"$progressfile" - echo "(Havgaard et al., 2007, PLoS Computational Biology 3:e193)." 1>>"$progressfile" - fi - if [ $distance = "foldalignglobal" ]; then - echo "Pairwise alignments were computed by FOLDALIGN (global)" 1>>"$progressfile" - echo "(Havgaard et al., 2007, PLoS Computational Biology 3:e193)." 1>>"$progressfile" - fi -# printf "\n" 1>>"$progressfile" - echo 'Strategy:' 1>>"$progressfile" - printf ' '$strategy 1>>"$progressfile" - echo ' ('$performance')' 1>>"$progressfile" - echo ' '$explanation 1>>"$progressfile" - echo '' 1>>"$progressfile" - echo "If unsure which option to use, try 'mafft --auto input > output'." 1>>"$progressfile" - echo "For more information, see 'mafft --help', 'mafft --man' and the mafft page." 1>>"$progressfile" - echo "" 1>>"$progressfile" - echo "The default gap scoring scheme has been changed in version 7.110 (2013 Oct)." 1>>"$progressfile" - echo "It tends to insert more gaps into gap-rich regions than previous versions." 1>>"$progressfile" - echo "To disable this change, add the --leavegappyregion option." 1>>"$progressfile" -# echo "If long gaps are expected, try 'mafft --ep 0.0 --auto input > output'." 1>>"$progressfile" -# echo "If the possibility of long gaps can be excluded, add '--ep 0.123'." 1>>"$progressfile" - if [ $distance = "localgenaf" -o $distance = "globalgenaf" ]; then - echo "" 1>>"$progressfile" - if [ $oldgenafparam -eq 1 ]; then - echo "Obsolete parameters used for this calculation." 1>>"$progressfile" - echo "Also try the new parameters for E-INS-i, by not specifying --oldgenafpair." 1>>"$progressfile" - else - echo "Parameters for the E-INS-i option have been changed in version 7.243 (2015 Jun)." 1>>"$progressfile" - echo "To switch to the old parameters, use --oldgenafpair, instead of --genafpair." 1>>"$progressfile" - fi - fi - echo '' 1>>"$progressfile" - - - if [ $pdblist != "/dev/null" -o $ownlist != "/dev/null" ]; then -# cat dasherr >>"$progressfile" - echo '' >>"$progressfile" - fi - - popd > /dev/null - - if [ "$outputopt" != "-f -l -1" -o "$windows" = "yes" ]; then # Windows deha kaigyo code wo f2cl de modosu. -# ln -s "$TMPFILE/order" _order$$ # f2cl ga space ari filename ni taiou shiteinainode -# cp "$TMPFILE/order" _order$$ # ln -s no error wo sakeru - if [ "$outputfile" = "" ]; then - "$prefix/f2cl" -n $namelength $outputopt < "$TMPFILE/pre" 2>"/dev/null" || exit 1 - else - "$prefix/f2cl" -n $namelength $outputopt < "$TMPFILE/pre" > "$outputfile" 2>"/dev/null" || exit 1 - fi -# rm _order$$ - else - if [ "$outputfile" = "" ]; then - cat < "$TMPFILE/pre" || exit 1 - else - cat < "$TMPFILE/pre" > "$outputfile" || exit 1 - fi - fi - - if [ $treeout -eq 1 ]; then - cp "$TMPFILE/infile.tree" "$infilename.tree" - fi - - if [ -s "$TMPFILE/GuideTree" ]; then # --merge no toki dake - cp "$TMPFILE/GuideTree" . - fi - - if [ $distout -eq 1 ]; then - cp "$TMPFILE/hat2" "$infilename.hat2" - fi - - if [ $npickup -ne 0 ]; then - cp "$TMPFILE/notused" "$infilename.notused" - fi - - if [ -s "$TMPFILE/_deletemap" ]; then - if [ "$mapoutfile" = "/dev/null" ]; then - cp "$TMPFILE/_deletemap" "$addfile.map" - else - cp "$TMPFILE/_deletemap" "$mapoutfile" - fi - fi - - exit 0; -fi - -prog="awk" - -#tmpawk=`which nawk 2>/dev/null | awk '{print $1}'` -#if [ -x "$tmpawk" ]; then -# prog="$tmpawk" -#fi -# -#tmpawk=`which gawk 2>/dev/null | awk '{print $1}'` -#if [ -x "$tmpawk" ]; then -# prog="$tmpawk" -#fi -# 2017/May/12, Windows no gawk wo sakeru tame - -#echo "prog="$prog 1>&2 - -umask 077 -( -$prog ' -BEGIN { - prefix = ENVIRON["prefix"]; - version = ENVIRON["version"]; - myself = ENVIRON["myself"]; - pwd = ENVIRON["mafft_working_dir"]; # from mafft.bat on windows - if( pwd == "" ) pwd = ENVIRON["PWD"]; - while( 1 ) - { - options = "" - printf( "\n" ) > "/dev/tty"; - printf( "---------------------------------------------------------------------\n" ) > "/dev/tty"; - printf( "\n" ) > "/dev/tty"; - printf( " MAFFT %s\n", version ) > "/dev/tty"; - printf( "\n" ) > "/dev/tty"; -# printf( " Copyright (c) 2002- Kazutaka Katoh\n" ) > "/dev/tty"; - printf( " MBE 30:772-780 (2013), NAR 30:3059-3066 (2002)\n" ) > "/dev/tty"; - printf( " https://mafft.cbrc.jp/alignment/software/\n" ) > "/dev/tty"; - printf( "---------------------------------------------------------------------\n" ) > "/dev/tty"; - printf( "\n" ) > "/dev/tty"; - - while( 1 ) - { - printf( "\n" ) > "/dev/tty"; - printf( "Input file? (FASTA format; Folder=%s)\n@ ", pwd ) > "/dev/tty"; - res = getline < "/dev/tty"; - close( "/dev/tty" ) - if( res == 0 || NF == 0 ) - continue; - infile = sprintf( "%s", $0 ); - - res = getline < infile; - close( infile ); - if( res == -1 ) - { - printf( "%s: No such file.\n\n", infile ) > "/dev/tty"; - printf( "Filename extension (eg., .txt) must be typed, if any.\n\n" ) > "/dev/tty"; - } - else if( res == 0 ) - printf( "%s: Empty.\n", infile ) > "/dev/tty"; - else - { - printf( "OK. infile = %s\n\n", infile ) > "/dev/tty"; - break; - } - } - nseq = 0; - - while( 1 ) - { - printf( "\n" ) > "/dev/tty"; - printf( "Output file?\n" ) > "/dev/tty"; - printf( "@ " ) > "/dev/tty"; - res = getline < "/dev/tty"; - close( "/dev/tty" ); - if( res == 0 || NF == 0 ) - continue; - else - { - outfile = sprintf( "%s", $0 ); - printf( "OK. outfile = %s\n\n", outfile ) > "/dev/tty"; - break; - } - } - - while( 1 ) - { - outargs = ""; - printf( "\n" ) > "/dev/tty"; - printf( "Output format?\n" ) > "/dev/tty"; - printf( " 1. Clustal format / Sorted\n" ) > "/dev/tty"; - printf( " 2. Clustal format / Input order\n" ) > "/dev/tty"; - printf( " 3. Fasta format / Sorted\n" ) > "/dev/tty"; - printf( " 4. Fasta format / Input order\n" ) > "/dev/tty"; - printf( " 5. Phylip format / Sorted\n" ) > "/dev/tty"; - printf( " 6. Phylip format / Input order\n" ) > "/dev/tty"; - printf( "@ " ) > "/dev/tty"; - res = getline < "/dev/tty"; - close( "/dev/tty" ); -# printf( "res=%d, NF=%d\n", res, NF ); - - resnum = 0 + $1; -# printf( "resnum=%d\n", resnum ); - - if( resnum < 1 || 6 < resnum ) - continue; - else - { - if( resnum == 1 ) - outargs = "--clustalout --reorder"; - else if( resnum == 2 ) - outargs = "--clustalout --inputorder"; - else if( resnum == 3 ) - outargs = "--reorder"; - else if( resnum == 4 ) - outargs = "--inputorder"; - else if( resnum == 5 ) - outargs = "--phylipout --reorder"; - else if( resnum == 6 ) - outargs = "--phylipout --inputorder"; - else - continue; - printf( "OK. arguments = %s\n\n", outargs ) > "/dev/tty"; - break; - } - } - - while( 1 ) - { - arguments = ""; - printf( "\n" ) > "/dev/tty"; - printf( "Strategy?\n" ) > "/dev/tty"; - printf( " 1. --auto\n" ) > "/dev/tty"; - printf( " 2. FFT-NS-1 (fast)\n" ) > "/dev/tty"; - printf( " 3. FFT-NS-2 (default)\n" ) > "/dev/tty"; - printf( " 4. G-INS-i (accurate)\n" ) > "/dev/tty"; - printf( " 5. L-INS-i (accurate)\n" ) > "/dev/tty"; - printf( " 6. E-INS-i (accurate)\n" ) > "/dev/tty"; - printf( "@ " ) > "/dev/tty"; - res = getline < "/dev/tty"; - close( "/dev/tty" ); -# printf( "res=%d, NF=%d\n", res, NF ); - - resnum = 0 + $1; -# printf( "resnum=%d\n", resnum ); - - if( resnum < 1 || 6 < resnum ) - continue; - else - { - if( resnum == 1 ) - arguments = "--auto"; - else if( resnum == 2 ) - arguments = "--retree 1"; - else if( resnum == 3 ) - arguments = "--retree 2"; - else if( resnum == 4 ) - arguments = "--globalpair --maxiterate 16"; - else if( resnum == 5 ) - arguments = "--localpair --maxiterate 16"; - else if( resnum == 6 ) - arguments = "--genafpair --maxiterate 16"; - else - arguments = sprintf( "%s", $0 ); - printf( "OK. arguments = %s %s\n\n", arguments, outargs ) > "/dev/tty"; - break; - } - } - - - while( 1 ) - { - printf( "\n" ) > "/dev/tty"; - printf( "Additional arguments? (--ep # --op # --kappa # etc)\n" ) > "/dev/tty"; - printf( "@ " ) > "/dev/tty"; - res = getline < "/dev/tty"; - close( "/dev/tty" ); - if( res == 0 || NF == 0 ) - { - break; - } - else - { - addargs = sprintf( "%s", $0 ); - printf( "OK. arguments = %s %s %s\n\n", addargs, arguments, outargs ) > "/dev/tty"; - break; - } - } - - arguments = sprintf( "%s %s %s", addargs, arguments, outargs ); - - print "" - command = sprintf( "\"%s\" %s \"%s\" > \"%s\"", myself, arguments, infile, outfile ); - gsub( /\\/, "/", command ); - - - printf( "command=\n%s\n", command ) > "/dev/tty"; - - - while( 1 ) - { - go = 0; - printf( "Type Y or just enter to run this command.\n" ) > "/dev/tty"; - printf( "@ " ) > "/dev/tty"; - res = getline < "/dev/tty"; - close( "/dev/tty" ); - if( res == 0 ) - continue; - else if( NF == 0 || $0 ~ /^[Yy]/ ) - { - go=1; - break; - } - else - break; - } - if( go ) break; - printf( "\n" ) > "/dev/tty"; - printf( "\n" ) > "/dev/tty"; - } - system( command ); - command = sprintf( "more \"%s\"", outfile ); - system( command ); - printf( "Press Enter to exit." ) > "/dev/tty"; - res = getline < "/dev/tty"; -} -' -) -exit 0; diff --git a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/addsingle b/aphylogeo/bin/mafft-linux64/mafftdir/libexec/addsingle deleted file mode 100755 index d0d1524f..00000000 Binary files a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/addsingle and /dev/null differ diff --git a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/contrafoldwrap b/aphylogeo/bin/mafft-linux64/mafftdir/libexec/contrafoldwrap deleted file mode 100755 index f784c9bf..00000000 Binary files a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/contrafoldwrap and /dev/null differ diff --git a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/countlen b/aphylogeo/bin/mafft-linux64/mafftdir/libexec/countlen deleted file mode 100755 index 224c96e0..00000000 Binary files a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/countlen and /dev/null differ diff --git a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/dash_alignments b/aphylogeo/bin/mafft-linux64/mafftdir/libexec/dash_alignments deleted file mode 100644 index 6047f59e..00000000 --- a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/dash_alignments +++ /dev/null @@ -1,483 +0,0 @@ -Query 3J5P_A||281||579 Template 3J5P_A||281||579 -QUERY EKNSVLEVIAYSSSETPNRHDMLLVEPLNRLLQDKWDRFVKRIFYFNFFVYCLYMIIFTAAAYYRPVEGLPPYKLKNTVGDYFRVTGEILSVSGGVYFFFRGIQYFLQRRPSLKSLFVDSYSEILFFVQSLFMLVSVVLYFSQRKEYVASMVFSLAMGWTNMLYYTRGFQQMGIYAVMIEKMILRDLCRFMFVYLVFLFGFSTAVVTLIEDGKYNSLYSTCLELFKFTIGMGDLEFTENYDFKAVFIILLLAYVILTYILLLNMLIALMGETVNKIAQESKNIWKLQRAITILDTEKSF -QUERY -TEMPL EKNSVLEVIAYSSSETPNRHDMLLVEPLNRLLQDKWDRFVKRIFYFNFFVYCLYMIIFTAAAYYRPVEGLPPYKLKNTVGDYFRVTGEILSVSGGVYFFFRGIQYFLQRRPSLKSLFVDSYSEILFFVQSLFMLVSVVLYFSQRKEYVASMVFSLAMGWTNMLYYTRGFQQMGIYAVMIEKMILRDLCRFMFVYLVFLFGFSTAVVTLIEDGKYNSLYSTCLELFKFTIGMGDLEFTENYDFKAVFIILLLAYVILTYILLLNMLIALMGETVNKIAQESKNIWKLQRAITILDTEKSF -TEMPL -Equivalence 99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 3J5P_A||283||585 Template 3J5P_A||283||585 -QUERY NSVLEVIAYSSSETPNRHDMLLVEPLNRLLQDKWDRFVKRIFYFNFFVYCLYMIIFTAAAYYRPVEGLPPYKLKNTVGDYFRVTGEILSVSGGVYFFFRGIQYFLQRRPSLKSLFVDSYSEILFFVQSLFMLVSVVLYFSQRKEYVASMVFSLAMGWTNMLYYTRGFQQMGIYAVMIEKMILRDLCRFMFVYLVFLFGFSTAVVTLIEDGKYNSLYSTCLELFKFTIGMGDLEFTENYDFKAVFIILLLAYVILTYILLLNMLIALMGETVNKIAQESKNIWKLQRAITILDTEKSFLKCMRK -QUERY -TEMPL NSVLEVIAYSSSETPNRHDMLLVEPLNRLLQDKWDRFVKRIFYFNFFVYCLYMIIFTAAAYYRPVEGLPPYKLKNTVGDYFRVTGEILSVSGGVYFFFRGIQYFLQRRPSLKSLFVDSYSEILFFVQSLFMLVSVVLYFSQRKEYVASMVFSLAMGWTNMLYYTRGFQQMGIYAVMIEKMILRDLCRFMFVYLVFLFGFSTAVVTLIEDGKYNSLYSTCLELFKFTIGMGDLEFTENYDFKAVFIILLLAYVILTYILLLNMLIALMGETVNKIAQESKNIWKLQRAITILDTEKSFLKCMRK -TEMPL -Equivalence 999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 3J9P_A||1089||1399 Template 3J9P_A||1089||1399 -QUERY YEPLTALNAMVQNNRIELLNHPVCKEYLLMKWLAYGFRAHMMNLGSYCLGLIPMTILVVNIKPGMAFNSTGIINETSDHSEILDTTNSYLIKTCMILVFLSSIFGYCKEAGQIFQQKRNYFMDISNVLEWIIYTTGIIFVLPLFVEIPAHLQWQCGAIAVYFYWMNFLLYLQRFENCGIFIVMLEVILKTLLRSTVVFIFLLLAFGLSFYILLNLQDPFSSPLLSIIQTFSMMLGDINYRESFLEPYLRNELAHPVLSFAQLVSFTIFVPIVLMNLLIGLAVGDIADVQKHASLKRIAMQVELHTSLEKKL -QUERY -TEMPL YEPLTALNAMVQNNRIELLNHPVCKEYLLMKWLAYGFRAHMMNLGSYCLGLIPMTILVVNIKPGMAFNSTGIINETSDHSEILDTTNSYLIKTCMILVFLSSIFGYCKEAGQIFQQKRNYFMDISNVLEWIIYTTGIIFVLPLFVEIPAHLQWQCGAIAVYFYWMNFLLYLQRFENCGIFIVMLEVILKTLLRSTVVFIFLLLAFGLSFYILLNLQDPFSSPLLSIIQTFSMMLGDINYRESFLEPYLRNELAHPVLSFAQLVSFTIFVPIVLMNLLIGLAVGDIADVQKHASLKRIAMQVELHTSLEKKL -TEMPL -Equivalence 99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 3J9P_A||1091||1408 Template 3J9P_A||1091||1408 -QUERY PLTALNAMVQNNRIELLNHPVCKEYLLMKWLAYGFRAHMMNLGSYCLGLIPMTILVVNIKPGMAFNSTGIINETSDHSEILDTTNSYLIKTCMILVFLSSIFGYCKEAGQIFQQKRNYFMDISNVLEWIIYTTGIIFVLPLFVEIPAHLQWQCGAIAVYFYWMNFLLYLQRFENCGIFIVMLEVILKTLLRSTVVFIFLLLAFGLSFYILLNLQDPFSSPLLSIIQTFSMMLGDINYRESFLEPYLRNELAHPVLSFAQLVSFTIFVPIVLMNLLIGLAVGDIADVQKHASLKRIAMQVELHTSLEKKLPLWFLRKVD -QUERY -TEMPL PLTALNAMVQNNRIELLNHPVCKEYLLMKWLAYGFRAHMMNLGSYCLGLIPMTILVVNIKPGMAFNSTGIINETSDHSEILDTTNSYLIKTCMILVFLSSIFGYCKEAGQIFQQKRNYFMDISNVLEWIIYTTGIIFVLPLFVEIPAHLQWQCGAIAVYFYWMNFLLYLQRFENCGIFIVMLEVILKTLLRSTVVFIFLLLAFGLSFYILLNLQDPFSSPLLSIIQTFSMMLGDINYRESFLEPYLRNELAHPVLSFAQLVSFTIFVPIVLMNLLIGLAVGDIADVQKHASLKRIAMQVELHTSLEKKLPLWFLRKVD -TEMPL -Equivalence 999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 3J9P_A||1092||1402 Template 3J9P_A||1092||1402 -QUERY LTALNAMVQNNRIELLNHPVCKEYLLMKWLAYGFRAHMMNLGSYCLGLIPMTILVVNIKPGMAFNSTGIINETSDHSEILDTTNSYLIKTCMILVFLSSIFGYCKEAGQIFQQKRNYFMDISNVLEWIIYTTGIIFVLPLFVEIPAHLQWQCGAIAVYFYWMNFLLYLQRFENCGIFIVMLEVILKTLLRSTVVFIFLLLAFGLSFYILLNLQDPFSSPLLSIIQTFSMMLGDINYRESFLEPYLRNELAHPVLSFAQLVSFTIFVPIVLMNLLIGLAVGDIADVQKHASLKRIAMQVELHTSLEKKLPLW -QUERY -TEMPL LTALNAMVQNNRIELLNHPVCKEYLLMKWLAYGFRAHMMNLGSYCLGLIPMTILVVNIKPGMAFNSTGIINETSDHSEILDTTNSYLIKTCMILVFLSSIFGYCKEAGQIFQQKRNYFMDISNVLEWIIYTTGIIFVLPLFVEIPAHLQWQCGAIAVYFYWMNFLLYLQRFENCGIFIVMLEVILKTLLRSTVVFIFLLLAFGLSFYILLNLQDPFSSPLLSIIQTFSMMLGDINYRESFLEPYLRNELAHPVLSFAQLVSFTIFVPIVLMNLLIGLAVGDIADVQKHASLKRIAMQVELHTSLEKKLPLW -TEMPL -Equivalence 99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 3J9P_A||1096||1410 Template 3J9P_A||1096||1410 -QUERY NAMVQNNRIELLNHPVCKEYLLMKWLAYGFRAHMMNLGSYCLGLIPMTILVVNIKPGMAFNSTGIINETSDHSEILDTTNSYLIKTCMILVFLSSIFGYCKEAGQIFQQKRNYFMDISNVLEWIIYTTGIIFVLPLFVEIPAHLQWQCGAIAVYFYWMNFLLYLQRFENCGIFIVMLEVILKTLLRSTVVFIFLLLAFGLSFYILLNLQDPFSSPLLSIIQTFSMMLGDINYRESFLEPYLRNELAHPVLSFAQLVSFTIFVPIVLMNLLIGLAVGDIADVQKHASLKRIAMQVELHTSLEKKLPLWFLRKVDQK -QUERY -TEMPL NAMVQNNRIELLNHPVCKEYLLMKWLAYGFRAHMMNLGSYCLGLIPMTILVVNIKPGMAFNSTGIINETSDHSEILDTTNSYLIKTCMILVFLSSIFGYCKEAGQIFQQKRNYFMDISNVLEWIIYTTGIIFVLPLFVEIPAHLQWQCGAIAVYFYWMNFLLYLQRFENCGIFIVMLEVILKTLLRSTVVFIFLLLAFGLSFYILLNLQDPFSSPLLSIIQTFSMMLGDINYRESFLEPYLRNELAHPVLSFAQLVSFTIFVPIVLMNLLIGLAVGDIADVQKHASLKRIAMQVELHTSLEKKLPLWFLRKVDQK -TEMPL -Equivalence 999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 5AN8_A||277||586 Template 5AN8_A||277||586 -QUERY NSVLEIIAFHSRSPHRHRMVVLEPLNKLLQAKWDRLIPRFCFNFLCYLVYMLIFTAVAYHQPALEKQGFPPLKATAGNSMLLLGHILILLGGVYLLLGQLWYFWRRRLFIWISFMDSYFEILFLLQALLTVLSQVLCFLAIEWYLPLLVSSLVLGWLNLLYYTRGFQHTGIYSVMIQKVILRDLLRFLLVYLVFLFGFAVALVSLSREAQEDEAPPYRSILDASLELFKFTIGMGELAFQEQLRFRGVVLLLLLAYVLLTYVLLLNMLIALMSETVNSVATDSWSIWKLQKAISVLEMENGYWWCRRKKQ -QUERY -TEMPL NSVLEIIAFHSRSPHRHRMVVLEPLNKLLQAKWDRLIPRFCFNFLCYLVYMLIFTAVAYHQPALEKQGFPPLKATAGNSMLLLGHILILLGGVYLLLGQLWYFWRRRLFIWISFMDSYFEILFLLQALLTVLSQVLCFLAIEWYLPLLVSSLVLGWLNLLYYTRGFQHTGIYSVMIQKVILRDLLRFLLVYLVFLFGFAVALVSLSREAQEDEAPPYRSILDASLELFKFTIGMGELAFQEQLRFRGVVLLLLLAYVLLTYVLLLNMLIALMSETVNSVATDSWSIWKLQKAISVLEMENGYWWCRRKKQ -TEMPL -Equivalence 9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 5IRX_A||286||584 Template 5IRX_A||286||584 -QUERY EKNSVLEVIAYSSSETPNRHDMLLVEPLNRLLQDKWDRFVKRIFYFNFFVYCLYMIIFTAAAYYRPVEGLPPYKLKNTVGDYFRVTGEILSVSGGVYFFFRGIQYFLQRRPSLKSLFVDSYSEILFFVQSLFMLVSVVLYFSQRKEYVASMVFSLAMGWTNMLYYTRGFQQMGIYAVMIEKMILRDLCRFMFVYLVFLFGFSTAVVTLIEDGKYNSLYSTCLELFKFTIGMGDLEFTENYDFKAVFIILLLAYVILTYILLLNMLIALMGETVNKIAQESKNIWKLQRAITILDTEKSF -QUERY -TEMPL EKNSVLEVIAYSSSETPNRHDMLLVEPLNRLLQDKWDRFVKRIFYFNFFVYCLYMIIFTAAAYYRPVEGLPPYKLKNTVGDYFRVTGEILSVSGGVYFFFRGIQYFLQRRPSLKSLFVDSYSEILFFVQSLFMLVSVVLYFSQRKEYVASMVFSLAMGWTNMLYYTRGFQQMGIYAVMIEKMILRDLCRFMFVYLVFLFGFSTAVVTLIEDGKYNSLYSTCLELFKFTIGMGDLEFTENYDFKAVFIILLLAYVILTYILLLNMLIALMGETVNKIAQESKNIWKLQRAITILDTEKSF -TEMPL -Equivalence 99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 5IRX_A||288||590 Template 5IRX_A||288||590 -QUERY NSVLEVIAYSSSETPNRHDMLLVEPLNRLLQDKWDRFVKRIFYFNFFVYCLYMIIFTAAAYYRPVEGLPPYKLKNTVGDYFRVTGEILSVSGGVYFFFRGIQYFLQRRPSLKSLFVDSYSEILFFVQSLFMLVSVVLYFSQRKEYVASMVFSLAMGWTNMLYYTRGFQQMGIYAVMIEKMILRDLCRFMFVYLVFLFGFSTAVVTLIEDGKYNSLYSTCLELFKFTIGMGDLEFTENYDFKAVFIILLLAYVILTYILLLNMLIALMGETVNKIAQESKNIWKLQRAITILDTEKSFLKCMRK -QUERY -TEMPL NSVLEVIAYSSSETPNRHDMLLVEPLNRLLQDKWDRFVKRIFYFNFFVYCLYMIIFTAAAYYRPVEGLPPYKLKNTVGDYFRVTGEILSVSGGVYFFFRGIQYFLQRRPSLKSLFVDSYSEILFFVQSLFMLVSVVLYFSQRKEYVASMVFSLAMGWTNMLYYTRGFQQMGIYAVMIEKMILRDLCRFMFVYLVFLFGFSTAVVTLIEDGKYNSLYSTCLELFKFTIGMGDLEFTENYDFKAVFIILLLAYVILTYILLLNMLIALMGETVNKIAQESKNIWKLQRAITILDTEKSFLKCMRK -TEMPL -Equivalence 999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 5IWK_A||287||613 Template 5IWK_A||287||613 -QUERY DDQSLLELIVTTKKREARQILDQTPVKELVSLKWKRYGRPYFCVLGAIYVLYIICFTMCCVYRPLKPRITNRTNPRDNTLLQQKLLQEAYVTPKDDLRLVGELVSIVGAVIILLVEIPDIFRLGVTRFFGQTILGGPFHVIIVTYAFMVLVTMVMRLTNSDGEVVPMSFALVLGWCNVMYFARGFQMLGPFTIMIQKMIFGDLMRFCWQMAVVILGFASAFYIIFQTEDPDELGHFYDYPMALFSTFELFLTIIDGPANYDVDLPFMYSITYAAFAIIATLLMLNLLIAMMGDTHWRVAHERDELWRAQVVATTVMLERKLPRCLWP -QUERY -TEMPL DDQSLLELIVTTKKREARQILDQTPVKELVSLKWKRYGRPYFCVLGAIYVLYIICFTMCCVYRPLKPRITNRTNPRDNTLLQQKLLQEAYVTPKDDLRLVGELVSIVGAVIILLVEIPDIFRLGVTRFFGQTILGGPFHVIIVTYAFMVLVTMVMRLTNSDGEVVPMSFALVLGWCNVMYFARGFQMLGPFTIMIQKMIFGDLMRFCWQMAVVILGFASAFYIIFQTEDPDELGHFYDYPMALFSTFELFLTIIDGPANYDVDLPFMYSITYAAFAIIATLLMLNLLIAMMGDTHWRVAHERDELWRAQVVATTVMLERKLPRCLWP -TEMPL -Equivalence 999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 5IWK_A||383||608 Template 5IWK_A||383||608 -QUERY LRLVGELVSIVGAVIILLVEIPDIFRLGVTRFFGQTILGGPFHVIIVTYAFMVLVTMVMRLTNSDGEVVPMSFALVLGWCNVMYFARGFQMLGPFTIMIQKMIFGDLMRFCWQMAVVILGFASAFYIIFQTEDPDELGHFYDYPMALFSTFELFLTIIDGPANYDVDLPFMYSITYAAFAIIATLLMLNLLIAMMGDTHWRVAHERDELWRAQVVATTVMLERKLP -QUERY -TEMPL LRLVGELVSIVGAVIILLVEIPDIFRLGVTRFFGQTILGGPFHVIIVTYAFMVLVTMVMRLTNSDGEVVPMSFALVLGWCNVMYFARGFQMLGPFTIMIQKMIFGDLMRFCWQMAVVILGFASAFYIIFQTEDPDELGHFYDYPMALFSTFELFLTIIDGPANYDVDLPFMYSITYAAFAIIATLLMLNLLIAMMGDTHWRVAHERDELWRAQVVATTVMLERKLP -TEMPL -Equivalence 9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 5K47_A||19||514 Template 5K47_A||19||514 -QUERY GTRLMEESSTNREKYLKSVLRELVTYLLFLIVLCILTYGMMSSNVYYYTRMMSQLFLDTPVSKTEKTNFKTLSSMEDFWKFTEGSLLDGLYWKMQPSNQTEADNRSFIFYENLLLGVPRIRQLRVRNGSCSIPQDLRDEIKECYDVYSVSSEDRAPFGPRNGTAWIYTSEKDLNGSSHWGIIATYSGAGYYLDLSRTREETAAQVASLKKNVWLDRGTRATFIDFSVYNANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAE -QUERY -TEMPL GTRLMEESSTNREKYLKSVLRELVTYLLFLIVLCILTYGMMSSNVYYYTRMMSQLFLDTPVSKTEKTNFKTLSSMEDFWKFTEGSLLDGLYWKMQPSNQTEADNRSFIFYENLLLGVPRIRQLRVRNGSCSIPQDLRDEIKECYDVYSVSSEDRAPFGPRNGTAWIYTSEKDLNGSSHWGIIATYSGAGYYLDLSRTREETAAQVASLKKNVWLDRGTRATFIDFSVYNANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAE -TEMPL -Equivalence 9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 5K47_A||20||521 Template 5K47_A||20||521 -QUERY TRLMEESSTNREKYLKSVLRELVTYLLFLIVLCILTYGMMSSNVYYYTRMMSQLFLDTPVSKTEKTNFKTLSSMEDFWKFTEGSLLDGLYWKMQPSNQTEADNRSFIFYENLLLGVPRIRQLRVRNGSCSIPQDLRDEIKECYDVYSVSSEDRAPFGPRNGTAWIYTSEKDLNGSSHWGIIATYSGAGYYLDLSRTREETAAQVASLKKNVWLDRGTRATFIDFSVYNANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLI -QUERY -TEMPL TRLMEESSTNREKYLKSVLRELVTYLLFLIVLCILTYGMMSSNVYYYTRMMSQLFLDTPVSKTEKTNFKTLSSMEDFWKFTEGSLLDGLYWKMQPSNQTEADNRSFIFYENLLLGVPRIRQLRVRNGSCSIPQDLRDEIKECYDVYSVSSEDRAPFGPRNGTAWIYTSEKDLNGSSHWGIIATYSGAGYYLDLSRTREETAAQVASLKKNVWLDRGTRATFIDFSVYNANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLI -TEMPL -Equivalence 9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 5K47_A||247||526 Template 5K47_A||247||526 -QUERY NANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLIRKGYH -QUERY -TEMPL NANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLIRKGYH -TEMPL -Equivalence 9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 5K47_A||2||537 Template 5K47_A||2||537 -QUERY PRVAWAERLVRGLRGLWGTRLMEESSTNREKYLKSVLRELVTYLLFLIVLCILTYGMMSSNVYYYTRMMSQLFLDTPVSKTEKTNFKTLSSMEDFWKFTEGSLLDGLYWKMQPSNQTEADNRSFIFYENLLLGVPRIRQLRVRNGSCSIPQDLRDEIKECYDVYSVSSEDRAPFGPRNGTAWIYTSEKDLNGSSHWGIIATYSGAGYYLDLSRTREETAAQVASLKKNVWLDRGTRATFIDFSVYNANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLIRKGYHKALVKLKLKKN -QUERY -TEMPL PRVAWAERLVRGLRGLWGTRLMEESSTNREKYLKSVLRELVTYLLFLIVLCILTYGMMSSNVYYYTRMMSQLFLDTPVSKTEKTNFKTLSSMEDFWKFTEGSLLDGLYWKMQPSNQTEADNRSFIFYENLLLGVPRIRQLRVRNGSCSIPQDLRDEIKECYDVYSVSSEDRAPFGPRNGTAWIYTSEKDLNGSSHWGIIATYSGAGYYLDLSRTREETAAQVASLKKNVWLDRGTRATFIDFSVYNANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLIRKGYHKALVKLKLKKN -TEMPL -Equivalence 99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 5K47_A||30||525 Template 5K47_A||30||525 -QUERY REKYLKSVLRELVTYLLFLIVLCILTYGMMSSNVYYYTRMMSQLFLDTPVSKTEKTNFKTLSSMEDFWKFTEGSLLDGLYWKMQPSNQTEADNRSFIFYENLLLGVPRIRQLRVRNGSCSIPQDLRDEIKECYDVYSVSSEDRAPFGPRNGTAWIYTSEKDLNGSSHWGIIATYSGAGYYLDLSRTREETAAQVASLKKNVWLDRGTRATFIDFSVYNANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLIRKGY -QUERY -TEMPL REKYLKSVLRELVTYLLFLIVLCILTYGMMSSNVYYYTRMMSQLFLDTPVSKTEKTNFKTLSSMEDFWKFTEGSLLDGLYWKMQPSNQTEADNRSFIFYENLLLGVPRIRQLRVRNGSCSIPQDLRDEIKECYDVYSVSSEDRAPFGPRNGTAWIYTSEKDLNGSSHWGIIATYSGAGYYLDLSRTREETAAQVASLKKNVWLDRGTRATFIDFSVYNANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLIRKGY -TEMPL -Equivalence 9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 5MKF_A||158||704 Template 5MKF_A||158||704 -QUERY EDQGPPCPSPVGGGDPLHRHLPLEGQPPRVAWAERLVRGLRGLWGTRLMEESSTNREKYLKSVLRELVTYLLFLIVLCILTYGMMSSNVYYYTRMMSQLFLDTPVSKTEKTNFKTLSSMEDFWKFTEGSLLDGLYWKMQPSNQTEADNRSFIFYENLLLGVPRIRQLRVRNGSCSIPQDLRDEIKECYDVYSVSSEDRAPFGPRNGTAWIYTSEKDLNGSSHWGIIATYSGAGYYLDLSRTREETAAQVASLKKNVWLDRGTRATFIDFSVYNANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLI -QUERY -TEMPL EDQGPPCPSPVGGGDPLHRHLPLEGQPPRVAWAERLVRGLRGLWGTRLMEESSTNREKYLKSVLRELVTYLLFLIVLCILTYGMMSSNVYYYTRMMSQLFLDTPVSKTEKTNFKTLSSMEDFWKFTEGSLLDGLYWKMQPSNQTEADNRSFIFYENLLLGVPRIRQLRVRNGSCSIPQDLRDEIKECYDVYSVSSEDRAPFGPRNGTAWIYTSEKDLNGSSHWGIIATYSGAGYYLDLSRTREETAAQVASLKKNVWLDRGTRATFIDFSVYNANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLI -TEMPL -Equivalence 9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 5MKF_A||185||720 Template 5MKF_A||185||720 -QUERY PRVAWAERLVRGLRGLWGTRLMEESSTNREKYLKSVLRELVTYLLFLIVLCILTYGMMSSNVYYYTRMMSQLFLDTPVSKTEKTNFKTLSSMEDFWKFTEGSLLDGLYWKMQPSNQTEADNRSFIFYENLLLGVPRIRQLRVRNGSCSIPQDLRDEIKECYDVYSVSSEDRAPFGPRNGTAWIYTSEKDLNGSSHWGIIATYSGAGYYLDLSRTREETAAQVASLKKNVWLDRGTRATFIDFSVYNANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLIRKGYHKALVKLKLKKN -QUERY -TEMPL PRVAWAERLVRGLRGLWGTRLMEESSTNREKYLKSVLRELVTYLLFLIVLCILTYGMMSSNVYYYTRMMSQLFLDTPVSKTEKTNFKTLSSMEDFWKFTEGSLLDGLYWKMQPSNQTEADNRSFIFYENLLLGVPRIRQLRVRNGSCSIPQDLRDEIKECYDVYSVSSEDRAPFGPRNGTAWIYTSEKDLNGSSHWGIIATYSGAGYYLDLSRTREETAAQVASLKKNVWLDRGTRATFIDFSVYNANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLIRKGYHKALVKLKLKKN -TEMPL -Equivalence 99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 5MKF_A||430||709 Template 5MKF_A||430||709 -QUERY NANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLIRKGYH -QUERY -TEMPL NANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLIRKGYH -TEMPL -Equivalence 9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 5TJA_A||3||217 Template 5TJA_A||3||217 -QUERY GLSNQLAVTFREENTIAFRHLFLLGYSDGADDTFAAYTREQLYQAIFHAVDQYLALPDVSLGRYAYVRGGGDPWTNGSGLALCQRYYHRGHVDPANDTFDIDPMVVTDCIQVDPPERPPPPPSDDLTLLESSSSYKNLTLKFHKLVNVTIHFRLKTINLQSLINNEIPDCYTFSVLITFDNKAHSGRIPISLETQAHIQECKHPSVFQHGDNSLE -QUERY -TEMPL GLSNQLAVTFREENTIAFRHLFLLGYSDGADDTFAAYTREQLYQAIFHAVDQYLALPDVSLGRYAYVRGGGDPWTNGSGLALCQRYYHRGHVDPANDTFDIDPMVVTDCIQVDPPERPPPPPSDDLTLLESSSSYKNLTLKFHKLVNVTIHFRLKTINLQSLINNEIPDCYTFSVLITFDNKAHSGRIPISLETQAHIQECKHPSVFQHGDNSLE -TEMPL -Equivalence 99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 5VKQ_A||1228||1596 Template 5VKQ_A||1228||1596 -QUERY DKRNVEFLDVLIENEQKEVIAHTVVQRYLQELWHGSLTWASWKILLLLVAFIVCPPVWIGFTFPMGHKFNKVPIIKFMSYLTSHIYLMIHLSIVGITPIYPVLRLSLVPYWYEVGLLIWLSGLLLFELTNPSDKSGLGSIKVLVLLLGMAGVGVHVSAFLFVSKEYWPTLVYCRNQCFALAFLLACVQILDFLSFHHLFGPWAIIIGDLLKDLARFLAVLAIFVFGFSMHIVALNQSFANFSPEDLRSFEKKNRNRGYFSDVRMHPINSFELLFFAVFGQTTTEQTQVDKIKNVATPTQPYWVEYLFKIVFGIYMLVSVVVLIQLLIAMMSDTYQRIQAQSDIEWKFGLSKLIRNMHRTTTAPSPLNLV -QUERY -TEMPL DKRNVEFLDVLIENEQKEVIAHTVVQRYLQELWHGSLTWASWKILLLLVAFIVCPPVWIGFTFPMGHKFNKVPIIKFMSYLTSHIYLMIHLSIVGITPIYPVLRLSLVPYWYEVGLLIWLSGLLLFELTNPSDKSGLGSIKVLVLLLGMAGVGVHVSAFLFVSKEYWPTLVYCRNQCFALAFLLACVQILDFLSFHHLFGPWAIIIGDLLKDLARFLAVLAIFVFGFSMHIVALNQSFANFSPEDLRSFEKKNRNRGYFSDVRMHPINSFELLFFAVFGQTTTEQTQVDKIKNVATPTQPYWVEYLFKIVFGIYMLVSVVVLIQLLIAMMSDTYQRIQAQSDIEWKFGLSKLIRNMHRTTTAPSPLNLV -TEMPL -Equivalence 999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 5W3S_A||14||541 Template 5W3S_A||14||541 -QUERY HEEENRCNFNQHTSPSEELLLEDQMRRKLKFFFMNPCEKFWARGRKPWKLAIQILKIAMVTIQLVLFGLSNQMVVAFKEENTVAFKHLFLKGYIDRMDDTYAVYTQSDVYDQIIFAVNQYLQLYQVSVGNHAYENKGTDQSAMAICQHFYKRGNIYPGNDTFDIDPEIETDCFFVEPDEPFHIGTPAENKLNLTLDFHRLLTVELQFKLKAINLQTVRHQELPDCYDFTLTITFDNKAHSGRIKISLDNDISIRECKDWHVSGSIQKNTHNMMIFDAFVILTCLVSLILCIRSVISGLQLQQEFVNFFLLHYKKDVSVSDQMEFVNGWYIMIIISDILTIIGSILKMEIQAKSLTSYDVCSILLGTSTMLVWLGVIRYLGFFAKYNLLILTLQAALPNVIRFCCCAAMIYLGYCFCGWIVLGPYHNKFRSLNMVSECLFSLINGDDMFATFAKMQQKSYLVWLFSRIYLYSFISLFIYMILSLFIALITDTYETIKHYQQDGFPETELRTFISECKDLPNSGKFRLED -QUERY -TEMPL HEEENRCNFNQHTSPSEELLLEDQMRRKLKFFFMNPCEKFWARGRKPWKLAIQILKIAMVTIQLVLFGLSNQMVVAFKEENTVAFKHLFLKGYIDRMDDTYAVYTQSDVYDQIIFAVNQYLQLYQVSVGNHAYENKGTDQSAMAICQHFYKRGNIYPGNDTFDIDPEIETDCFFVEPDEPFHIGTPAENKLNLTLDFHRLLTVELQFKLKAINLQTVRHQELPDCYDFTLTITFDNKAHSGRIKISLDNDISIRECKDWHVSGSIQKNTHNMMIFDAFVILTCLVSLILCIRSVISGLQLQQEFVNFFLLHYKKDVSVSDQMEFVNGWYIMIIISDILTIIGSILKMEIQAKSLTSYDVCSILLGTSTMLVWLGVIRYLGFFAKYNLLILTLQAALPNVIRFCCCAAMIYLGYCFCGWIVLGPYHNKFRSLNMVSECLFSLINGDDMFATFAKMQQKSYLVWLFSRIYLYSFISLFIYMILSLFIALITDTYETIKHYQQDGFPETELRTFISECKDLPNSGKFRLED -TEMPL -Equivalence 999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 5W3S_A||28||546 Template 5W3S_A||28||546 -QUERY PSEELLLEDQMRRKLKFFFMNPCEKFWARGRKPWKLAIQILKIAMVTIQLVLFGLSNQMVVAFKEENTVAFKHLFLKGYIDRMDDTYAVYTQSDVYDQIIFAVNQYLQLYQVSVGNHAYENKGTDQSAMAICQHFYKRGNIYPGNDTFDIDPEIETDCFFVEPDEPFHIGTPAENKLNLTLDFHRLLTVELQFKLKAINLQTVRHQELPDCYDFTLTITFDNKAHSGRIKISLDNDISIRECKDWHVSGSIQKNTHNMMIFDAFVILTCLVSLILCIRSVISGLQLQQEFVNFFLLHYKKDVSVSDQMEFVNGWYIMIIISDILTIIGSILKMEIQAKSLTSYDVCSILLGTSTMLVWLGVIRYLGFFAKYNLLILTLQAALPNVIRFCCCAAMIYLGYCFCGWIVLGPYHNKFRSLNMVSECLFSLINGDDMFATFAKMQQKSYLVWLFSRIYLYSFISLFIYMILSLFIALITDTYETIKHYQQDGFPETELRTFISECKDLPNSGKFRLEDDPPVS -QUERY -TEMPL PSEELLLEDQMRRKLKFFFMNPCEKFWARGRKPWKLAIQILKIAMVTIQLVLFGLSNQMVVAFKEENTVAFKHLFLKGYIDRMDDTYAVYTQSDVYDQIIFAVNQYLQLYQVSVGNHAYENKGTDQSAMAICQHFYKRGNIYPGNDTFDIDPEIETDCFFVEPDEPFHIGTPAENKLNLTLDFHRLLTVELQFKLKAINLQTVRHQELPDCYDFTLTITFDNKAHSGRIKISLDNDISIRECKDWHVSGSIQKNTHNMMIFDAFVILTCLVSLILCIRSVISGLQLQQEFVNFFLLHYKKDVSVSDQMEFVNGWYIMIIISDILTIIGSILKMEIQAKSLTSYDVCSILLGTSTMLVWLGVIRYLGFFAKYNLLILTLQAALPNVIRFCCCAAMIYLGYCFCGWIVLGPYHNKFRSLNMVSECLFSLINGDDMFATFAKMQQKSYLVWLFSRIYLYSFISLFIYMILSLFIALITDTYETIKHYQQDGFPETELRTFISECKDLPNSGKFRLEDDPPVS -TEMPL -Equivalence 999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 5WJ9_A||16||557 Template 5WJ9_A||16||557 -QUERY LTPNPGYGTQAGPSPAPPTPPEEEDLRRRLKYFFMSPCDKFRAKGRKPCKLMLQVVKILVVTVQLILFGLSNQLAVTFREENTIAFRHLFLLGYSDGADDTFAAYTREQLYQAIFHAVDQYLALPDVSLGRYAYVRGGGDPWTNGSGLALCQRYYHRGHVDPANDTFDIDPMVVTDCIQVDPPERPPPPPSDDLTLLESSSSYKNLTLKFHKLVNVTIHFRLKTINLQSLINNEIPDCYTFSVLITFDNKAHSGRIPISLETQAHIQECKHPSVFQHGDNSFRLLFDVVVILTCSLSFLLCARSLLRGFLLQNEFVGFMWRQRGRVISLWERLEFVNGWYILLVTSDVLTISGTIMKIGIEAKNLASYDVCSILLGTSTLLVWVGVIRYLTFFHNYNILIATLRVALPSVMRFCCCVAVIYLGYCFCGWIVLGPYHVKFRSLSMVSECLFSLINGDDMFVTFAAMQAQQGRSSLVWLFSQLYLYSFISLFIYMVLSLFIALITGAYDTIKHPGGAGAEESELQAYIAQCQDSPTSGKFRRGS -QUERY -TEMPL LTPNPGYGTQAGPSPAPPTPPEEEDLRRRLKYFFMSPCDKFRAKGRKPCKLMLQVVKILVVTVQLILFGLSNQLAVTFREENTIAFRHLFLLGYSDGADDTFAAYTREQLYQAIFHAVDQYLALPDVSLGRYAYVRGGGDPWTNGSGLALCQRYYHRGHVDPANDTFDIDPMVVTDCIQVDPPERPPPPPSDDLTLLESSSSYKNLTLKFHKLVNVTIHFRLKTINLQSLINNEIPDCYTFSVLITFDNKAHSGRIPISLETQAHIQECKHPSVFQHGDNSFRLLFDVVVILTCSLSFLLCARSLLRGFLLQNEFVGFMWRQRGRVISLWERLEFVNGWYILLVTSDVLTISGTIMKIGIEAKNLASYDVCSILLGTSTLLVWVGVIRYLTFFHNYNILIATLRVALPSVMRFCCCVAVIYLGYCFCGWIVLGPYHVKFRSLSMVSECLFSLINGDDMFVTFAAMQAQQGRSSLVWLFSQLYLYSFISLFIYMVLSLFIALITGAYDTIKHPGGAGAEESELQAYIAQCQDSPTSGKFRRGS -TEMPL -Equivalence 99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 5WPV_A||16||557 Template 5WPV_A||16||557 -QUERY LTPNPGYGTQVGTSPAPTTPTEEEDLRRRLKYFFMSPCDKFRAKGRKPCKLMLQVVKILVVTVQLILFGLSNQLVVTFREENTIAFRHLFLLGYSDGSDDTFAAYTQEQLYQAIFYAVDQYLILPEISLGRYAYVRGGGGPWANGSALALCQRYYHRGHVDPANDTFDIDPRVVTDCIQVDPPDRPPDIPSEDLDFLDGSASYKNLTLKFHKLINVTIHFQLKTINLQSLINNEIPDCYTFSILITFDNKAHSGRIPIRLETKTHIQECKHPSVSRHGDNSFRLLFDVVVILTCSLSFLLCARSLLRGFLLQNEFVVFMWRRRGREISLWERLEFVNGWYILLVTSDVLTISGTVMKIGIEAKNLASYDVCSILLGTSTLLVWVGVIRYLTFFHKYNILIATLRVALPSVMRFCCCVAVIYLGYCFCGWIVLGPYHVKFRSLSMVSECLFSLINGDDMFVTFAAMQAQQGHSSLVWLFSQLYLYSFISLFIYMVLSLFIALITGAYDTIKHPGGTGTEKSELQAYIEQCQDSPTSGKFRRGS -QUERY -TEMPL LTPNPGYGTQVGTSPAPTTPTEEEDLRRRLKYFFMSPCDKFRAKGRKPCKLMLQVVKILVVTVQLILFGLSNQLVVTFREENTIAFRHLFLLGYSDGSDDTFAAYTQEQLYQAIFYAVDQYLILPEISLGRYAYVRGGGGPWANGSALALCQRYYHRGHVDPANDTFDIDPRVVTDCIQVDPPDRPPDIPSEDLDFLDGSASYKNLTLKFHKLINVTIHFQLKTINLQSLINNEIPDCYTFSILITFDNKAHSGRIPIRLETKTHIQECKHPSVSRHGDNSFRLLFDVVVILTCSLSFLLCARSLLRGFLLQNEFVVFMWRRRGREISLWERLEFVNGWYILLVTSDVLTISGTVMKIGIEAKNLASYDVCSILLGTSTLLVWVGVIRYLTFFHKYNILIATLRVALPSVMRFCCCVAVIYLGYCFCGWIVLGPYHVKFRSLSMVSECLFSLINGDDMFVTFAAMQAQQGHSSLVWLFSQLYLYSFISLFIYMVLSLFIALITGAYDTIKHPGGTGTEKSELQAYIEQCQDSPTSGKFRRGS -TEMPL -Equivalence 99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 5Z1W_A||127||515 Template 5Z1W_A||127||515 -QUERY YENLLLGAPRLRQLRVRNDSCVVHEDFREDILNCYDVYSPDKEDQLPFGPQNGTAWTYHSQNELGGSSHWGRLTSYSGGGYYLDLPGSRQASAEALQGLQEGLWLDRGTRVVFIDFSVYNANINLFCILRLVVEFPATGGTIPSWQIRTVKLIRYVNNWDFFIVGCEVVFCVFIFYYVVEEILEIHLHRLRYLSSVWNILDLVVILLSIVAVGFHIFRTLEVNRLMGKLLQQPDTYADFEFLAFWQTQYNNMNAVNLFFAWIKIFKYISFNKTMTQLSSTLARCAKDILGFAIMFFIVFFAYAQLGYLLFGTQVENFSTFVKCIFTQFRIILGDFDYNAIDNANRILGPVYFVTYVFFVFFVLLNMFLAIINDTYSEVKEELAGQKDQL -QUERY -TEMPL YENLLLGAPRLRQLRVRNDSCVVHEDFREDILNCYDVYSPDKEDQLPFGPQNGTAWTYHSQNELGGSSHWGRLTSYSGGGYYLDLPGSRQASAEALQGLQEGLWLDRGTRVVFIDFSVYNANINLFCILRLVVEFPATGGTIPSWQIRTVKLIRYVNNWDFFIVGCEVVFCVFIFYYVVEEILEIHLHRLRYLSSVWNILDLVVILLSIVAVGFHIFRTLEVNRLMGKLLQQPDTYADFEFLAFWQTQYNNMNAVNLFFAWIKIFKYISFNKTMTQLSSTLARCAKDILGFAIMFFIVFFAYAQLGYLLFGTQVENFSTFVKCIFTQFRIILGDFDYNAIDNANRILGPVYFVTYVFFVFFVLLNMFLAIINDTYSEVKEELAGQKDQL -TEMPL -Equivalence 99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 5Z1W_A||13||506 Template 5Z1W_A||13||506 -QUERY SIRGLWGTTLTENTAENRELYVKTTLRELVVYIVFLVDICLLTYGMTSSSAYYYTKVMSELFLHTPSDSGVSFQTISSMSDFWDFAQGPLLDSLYWTKWYNNQSLGRGSHSFIYYENLLLGAPRLRQLRVRNDSCVVHEDFREDILNCYDVYSPDKEDQLPFGPQNGTAWTYHSQNELGGSSHWGRLTSYSGGGYYLDLPGSRQASAEALQGLQEGLWLDRGTRVVFIDFSVYNANINLFCILRLVVEFPATGGTIPSWQIRTVKLIRYVNNWDFFIVGCEVVFCVFIFYYVVEEILEIHLHRLRYLSSVWNILDLVVILLSIVAVGFHIFRTLEVNRLMGKLLQQPDTYADFEFLAFWQTQYNNMNAVNLFFAWIKIFKYISFNKTMTQLSSTLARCAKDILGFAIMFFIVFFAYAQLGYLLFGTQVENFSTFVKCIFTQFRIILGDFDYNAIDNANRILGPVYFVTYVFFVFFVLLNMFLAIINDTYSEVKE -QUERY -TEMPL SIRGLWGTTLTENTAENRELYVKTTLRELVVYIVFLVDICLLTYGMTSSSAYYYTKVMSELFLHTPSDSGVSFQTISSMSDFWDFAQGPLLDSLYWTKWYNNQSLGRGSHSFIYYENLLLGAPRLRQLRVRNDSCVVHEDFREDILNCYDVYSPDKEDQLPFGPQNGTAWTYHSQNELGGSSHWGRLTSYSGGGYYLDLPGSRQASAEALQGLQEGLWLDRGTRVVFIDFSVYNANINLFCILRLVVEFPATGGTIPSWQIRTVKLIRYVNNWDFFIVGCEVVFCVFIFYYVVEEILEIHLHRLRYLSSVWNILDLVVILLSIVAVGFHIFRTLEVNRLMGKLLQQPDTYADFEFLAFWQTQYNNMNAVNLFFAWIKIFKYISFNKTMTQLSSTLARCAKDILGFAIMFFIVFFAYAQLGYLLFGTQVENFSTFVKCIFTQFRIILGDFDYNAIDNANRILGPVYFVTYVFFVFFVLLNMFLAIINDTYSEVKE -TEMPL -Equivalence 99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 5Z1W_A||246||537 Template 5Z1W_A||246||537 -QUERY NANINLFCILRLVVEFPATGGTIPSWQIRTVKLIRYVNNWDFFIVGCEVVFCVFIFYYVVEEILEIHLHRLRYLSSVWNILDLVVILLSIVAVGFHIFRTLEVNRLMGKLLQQPDTYADFEFLAFWQTQYNNMNAVNLFFAWIKIFKYISFNKTMTQLSSTLARCAKDILGFAIMFFIVFFAYAQLGYLLFGTQVENFSTFVKCIFTQFRIILGDFDYNAIDNANRILGPVYFVTYVFFVFFVLLNMFLAIINDTYSEVKEELAGQKDQLQLSDFLKQSYNKTLLRLRLRKE -QUERY -TEMPL NANINLFCILRLVVEFPATGGTIPSWQIRTVKLIRYVNNWDFFIVGCEVVFCVFIFYYVVEEILEIHLHRLRYLSSVWNILDLVVILLSIVAVGFHIFRTLEVNRLMGKLLQQPDTYADFEFLAFWQTQYNNMNAVNLFFAWIKIFKYISFNKTMTQLSSTLARCAKDILGFAIMFFIVFFAYAQLGYLLFGTQVENFSTFVKCIFTQFRIILGDFDYNAIDNANRILGPVYFVTYVFFVFFVLLNMFLAIINDTYSEVKEELAGQKDQLQLSDFLKQSYNKTLLRLRLRKE -TEMPL -Equivalence 9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 5Z1W_A||29||447 Template 5Z1W_A||29||447 -QUERY NRELYVKTTLRELVVYIVFLVDICLLTYGMTSSSAYYYTKVMSELFLHTPSDSGVSFQTISSMSDFWDFAQGPLLDSLYWTKWYNNQSLGRGSHSFIYYENLLLGAPRLRQLRVRNDSCVVHEDFREDILNCYDVYSPDKEDQLPFGPQNGTAWTYHSQNELGGSSHWGRLTSYSGGGYYLDLPGSRQASAEALQGLQEGLWLDRGTRVVFIDFSVYNANINLFCILRLVVEFPATGGTIPSWQIRTVKLIRYVNNWDFFIVGCEVVFCVFIFYYVVEEILEIHLHRLRYLSSVWNILDLVVILLSIVAVGFHIFRTLEVNRLMGKLLQQPDTYADFEFLAFWQTQYNNMNAVNLFFAWIKIFKYISFNKTMTQLSSTLARCAKDILGFAIMFFIVFFAYAQLGYLLFGTQVENFSTFV -QUERY -TEMPL NRELYVKTTLRELVVYIVFLVDICLLTYGMTSSSAYYYTKVMSELFLHTPSDSGVSFQTISSMSDFWDFAQGPLLDSLYWTKWYNNQSLGRGSHSFIYYENLLLGAPRLRQLRVRNDSCVVHEDFREDILNCYDVYSPDKEDQLPFGPQNGTAWTYHSQNELGGSSHWGRLTSYSGGGYYLDLPGSRQASAEALQGLQEGLWLDRGTRVVFIDFSVYNANINLFCILRLVVEFPATGGTIPSWQIRTVKLIRYVNNWDFFIVGCEVVFCVFIFYYVVEEILEIHLHRLRYLSSVWNILDLVVILLSIVAVGFHIFRTLEVNRLMGKLLQQPDTYADFEFLAFWQTQYNNMNAVNLFFAWIKIFKYISFNKTMTQLSSTLARCAKDILGFAIMFFIVFFAYAQLGYLLFGTQVENFSTFV -TEMPL -Equivalence 99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 5Z1W_A||41||508 Template 5Z1W_A||41||508 -QUERY LVVYIVFLVDICLLTYGMTSSSAYYYTKVMSELFLHTPSDSGVSFQTISSMSDFWDFAQGPLLDSLYWTKWYNNQSLGRGSHSFIYYENLLLGAPRLRQLRVRNDSCVVHEDFREDILNCYDVYSPDKEDQLPFGPQNGTAWTYHSQNELGGSSHWGRLTSYSGGGYYLDLPGSRQASAEALQGLQEGLWLDRGTRVVFIDFSVYNANINLFCILRLVVEFPATGGTIPSWQIRTVKLIRYVNNWDFFIVGCEVVFCVFIFYYVVEEILEIHLHRLRYLSSVWNILDLVVILLSIVAVGFHIFRTLEVNRLMGKLLQQPDTYADFEFLAFWQTQYNNMNAVNLFFAWIKIFKYISFNKTMTQLSSTLARCAKDILGFAIMFFIVFFAYAQLGYLLFGTQVENFSTFVKCIFTQFRIILGDFDYNAIDNANRILGPVYFVTYVFFVFFVLLNMFLAIINDTYSEVKEEL -QUERY -TEMPL LVVYIVFLVDICLLTYGMTSSSAYYYTKVMSELFLHTPSDSGVSFQTISSMSDFWDFAQGPLLDSLYWTKWYNNQSLGRGSHSFIYYENLLLGAPRLRQLRVRNDSCVVHEDFREDILNCYDVYSPDKEDQLPFGPQNGTAWTYHSQNELGGSSHWGRLTSYSGGGYYLDLPGSRQASAEALQGLQEGLWLDRGTRVVFIDFSVYNANINLFCILRLVVEFPATGGTIPSWQIRTVKLIRYVNNWDFFIVGCEVVFCVFIFYYVVEEILEIHLHRLRYLSSVWNILDLVVILLSIVAVGFHIFRTLEVNRLMGKLLQQPDTYADFEFLAFWQTQYNNMNAVNLFFAWIKIFKYISFNKTMTQLSSTLARCAKDILGFAIMFFIVFFAYAQLGYLLFGTQVENFSTFVKCIFTQFRIILGDFDYNAIDNANRILGPVYFVTYVFFVFFVLLNMFLAIINDTYSEVKEEL -TEMPL -Equivalence 999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 5Z1W_A||9||528 Template 5Z1W_A||9||528 -QUERY HICRSIRGLWGTTLTENTAENRELYVKTTLRELVVYIVFLVDICLLTYGMTSSSAYYYTKVMSELFLHTPSDSGVSFQTISSMSDFWDFAQGPLLDSLYWTKWYNNQSLGRGSHSFIYYENLLLGAPRLRQLRVRNDSCVVHEDFREDILNCYDVYSPDKEDQLPFGPQNGTAWTYHSQNELGGSSHWGRLTSYSGGGYYLDLPGSRQASAEALQGLQEGLWLDRGTRVVFIDFSVYNANINLFCILRLVVEFPATGGTIPSWQIRTVKLIRYVNNWDFFIVGCEVVFCVFIFYYVVEEILEIHLHRLRYLSSVWNILDLVVILLSIVAVGFHIFRTLEVNRLMGKLLQQPDTYADFEFLAFWQTQYNNMNAVNLFFAWIKIFKYISFNKTMTQLSSTLARCAKDILGFAIMFFIVFFAYAQLGYLLFGTQVENFSTFVKCIFTQFRIILGDFDYNAIDNANRILGPVYFVTYVFFVFFVLLNMFLAIINDTYSEVKEELAGQKDQLQLSDFLKQSYNKT -QUERY -TEMPL HICRSIRGLWGTTLTENTAENRELYVKTTLRELVVYIVFLVDICLLTYGMTSSSAYYYTKVMSELFLHTPSDSGVSFQTISSMSDFWDFAQGPLLDSLYWTKWYNNQSLGRGSHSFIYYENLLLGAPRLRQLRVRNDSCVVHEDFREDILNCYDVYSPDKEDQLPFGPQNGTAWTYHSQNELGGSSHWGRLTSYSGGGYYLDLPGSRQASAEALQGLQEGLWLDRGTRVVFIDFSVYNANINLFCILRLVVEFPATGGTIPSWQIRTVKLIRYVNNWDFFIVGCEVVFCVFIFYYVVEEILEIHLHRLRYLSSVWNILDLVVILLSIVAVGFHIFRTLEVNRLMGKLLQQPDTYADFEFLAFWQTQYNNMNAVNLFFAWIKIFKYISFNKTMTQLSSTLARCAKDILGFAIMFFIVFFAYAQLGYLLFGTQVENFSTFVKCIFTQFRIILGDFDYNAIDNANRILGPVYFVTYVFFVFFVLLNMFLAIINDTYSEVKEELAGQKDQLQLSDFLKQSYNKT -TEMPL -Equivalence 9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 5Z96_A||286||659 Template 5Z96_A||286||659 -QUERY LARLKLAIKYRQKEFVAQPNCQQLLASRWYDEFPGWRRRHWAVKMVTCFIIGLLFPVFSVCYLIAPKSPLGLFIRKPFIKFICHTASYLTFLFLLLLASQHIDRSDLNRQGPPPTIVEWMILPWVLGFIWGEIKQMWDGGLQDYIHDWWNLMDFVMNSLYLATISLKIVAFVKYSALNPRESWDMWHPTLVAEALFAIANIFSSLRLISLFTANSHLGPLQISLGRMLLDILKFLFIYCLVLLAFANGLNQLYFYYEETKGLSCKGIRCEKQNNAFSTLFETLQSLFWSIFGLINLYVTNVKAQHEFTEFVGATMFGTYNVISLVVLLNMLIAMMNNSYQLIADHADIEWKFARTKLWMSYFEEGGTLPTPFNV -QUERY -TEMPL LARLKLAIKYRQKEFVAQPNCQQLLASRWYDEFPGWRRRHWAVKMVTCFIIGLLFPVFSVCYLIAPKSPLGLFIRKPFIKFICHTASYLTFLFLLLLASQHIDRSDLNRQGPPPTIVEWMILPWVLGFIWGEIKQMWDGGLQDYIHDWWNLMDFVMNSLYLATISLKIVAFVKYSALNPRESWDMWHPTLVAEALFAIANIFSSLRLISLFTANSHLGPLQISLGRMLLDILKFLFIYCLVLLAFANGLNQLYFYYEETKGLSCKGIRCEKQNNAFSTLFETLQSLFWSIFGLINLYVTNVKAQHEFTEFVGATMFGTYNVISLVVLLNMLIAMMNNSYQLIADHADIEWKFARTKLWMSYFEEGGTLPTPFNV -TEMPL -Equivalence 99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 5Z96_A||289||660 Template 5Z96_A||289||660 -QUERY LKLAIKYRQKEFVAQPNCQQLLASRWYDEFPGWRRRHWAVKMVTCFIIGLLFPVFSVCYLIAPKSPLGLFIRKPFIKFICHTASYLTFLFLLLLASQHIDRSDLNRQGPPPTIVEWMILPWVLGFIWGEIKQMWDGGLQDYIHDWWNLMDFVMNSLYLATISLKIVAFVKYSALNPRESWDMWHPTLVAEALFAIANIFSSLRLISLFTANSHLGPLQISLGRMLLDILKFLFIYCLVLLAFANGLNQLYFYYEETKGLSCKGIRCEKQNNAFSTLFETLQSLFWSIFGLINLYVTNVKAQHEFTEFVGATMFGTYNVISLVVLLNMLIAMMNNSYQLIADHADIEWKFARTKLWMSYFEEGGTLPTPFNVI -QUERY -TEMPL LKLAIKYRQKEFVAQPNCQQLLASRWYDEFPGWRRRHWAVKMVTCFIIGLLFPVFSVCYLIAPKSPLGLFIRKPFIKFICHTASYLTFLFLLLLASQHIDRSDLNRQGPPPTIVEWMILPWVLGFIWGEIKQMWDGGLQDYIHDWWNLMDFVMNSLYLATISLKIVAFVKYSALNPRESWDMWHPTLVAEALFAIANIFSSLRLISLFTANSHLGPLQISLGRMLLDILKFLFIYCLVLLAFANGLNQLYFYYEETKGLSCKGIRCEKQNNAFSTLFETLQSLFWSIFGLINLYVTNVKAQHEFTEFVGATMFGTYNVISLVVLLNMLIAMMNNSYQLIADHADIEWKFARTKLWMSYFEEGGTLPTPFNVI -TEMPL -Equivalence 999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 5Z96_A||290||663 Template 5Z96_A||290||663 -QUERY KLAIKYRQKEFVAQPNCQQLLASRWYDEFPGWRRRHWAVKMVTCFIIGLLFPVFSVCYLIAPKSPLGLFIRKPFIKFICHTASYLTFLFLLLLASQHIDRSDLNRQGPPPTIVEWMILPWVLGFIWGEIKQMWDGGLQDYIHDWWNLMDFVMNSLYLATISLKIVAFVKYSALNPRESWDMWHPTLVAEALFAIANIFSSLRLISLFTANSHLGPLQISLGRMLLDILKFLFIYCLVLLAFANGLNQLYFYYEETKGLSCKGIRCEKQNNAFSTLFETLQSLFWSIFGLINLYVTNVKAQHEFTEFVGATMFGTYNVISLVVLLNMLIAMMNNSYQLIADHADIEWKFARTKLWMSYFEEGGTLPTPFNVIPSP -QUERY -TEMPL KLAIKYRQKEFVAQPNCQQLLASRWYDEFPGWRRRHWAVKMVTCFIIGLLFPVFSVCYLIAPKSPLGLFIRKPFIKFICHTASYLTFLFLLLLASQHIDRSDLNRQGPPPTIVEWMILPWVLGFIWGEIKQMWDGGLQDYIHDWWNLMDFVMNSLYLATISLKIVAFVKYSALNPRESWDMWHPTLVAEALFAIANIFSSLRLISLFTANSHLGPLQISLGRMLLDILKFLFIYCLVLLAFANGLNQLYFYYEETKGLSCKGIRCEKQNNAFSTLFETLQSLFWSIFGLINLYVTNVKAQHEFTEFVGATMFGTYNVISLVVLLNMLIAMMNNSYQLIADHADIEWKFARTKLWMSYFEEGGTLPTPFNVIPSP -TEMPL -Equivalence 99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 5ZX5_A||814||1056 Template 5ZX5_A||814||1056 -QUERY FKEVKILDSSDGKNEMEIHIKSKKLPITRKFYAFYHAPIVKFWFNTLAYLGFLMLYTFVVLVKMEQLPSVQEWIVIAYIFTYAIEKVREVFMSEAGKISQKIKVWFSDYFNVSDTIAIISFFVGFGLRFGAKWNYINAYDNHVFVAGRLIYCLNIIFWYVRLLDFLAVNQQAGPYVMMIGKMVANMFYIVVIMALVLLSFGVPRKAILYPHEEPSWSLAKDIVFHPYWMIFGEVYAYEIDVCA -QUERY -TEMPL FKEVKILDSSDGKNEMEIHIKSKKLPITRKFYAFYHAPIVKFWFNTLAYLGFLMLYTFVVLVKMEQLPSVQEWIVIAYIFTYAIEKVREVFMSEAGKISQKIKVWFSDYFNVSDTIAIISFFVGFGLRFGAKWNYINAYDNHVFVAGRLIYCLNIIFWYVRLLDFLAVNQQAGPYVMMIGKMVANMFYIVVIMALVLLSFGVPRKAILYPHEEPSWSLAKDIVFHPYWMIFGEVYAYEIDVCA -TEMPL -Equivalence 999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 5ZX5_A||820||1131 Template 5ZX5_A||820||1131 -QUERY LDSSDGKNEMEIHIKSKKLPITRKFYAFYHAPIVKFWFNTLAYLGFLMLYTFVVLVKMEQLPSVQEWIVIAYIFTYAIEKVREVFMSEAGKISQKIKVWFSDYFNVSDTIAIISFFVGFGLRFGAKWNYINAYDNHVFVAGRLIYCLNIIFWYVRLLDFLAVNQQAGPYVMMIGKMVANMFYIVVIMALVLLSFGVPRKAILYPHEEPSWSLAKDIVFHPYWMIFGEVYAYEIDVCANDSTLPTICGPGTWLTPFLQAVYLFVQYIIMVNLLIAFFNNVYLQVKAISNIVWKYQRYHFIMAYHEKPVLPPPL -QUERY -TEMPL LDSSDGKNEMEIHIKSKKLPITRKFYAFYHAPIVKFWFNTLAYLGFLMLYTFVVLVKMEQLPSVQEWIVIAYIFTYAIEKVREVFMSEAGKISQKIKVWFSDYFNVSDTIAIISFFVGFGLRFGAKWNYINAYDNHVFVAGRLIYCLNIIFWYVRLLDFLAVNQQAGPYVMMIGKMVANMFYIVVIMALVLLSFGVPRKAILYPHEEPSWSLAKDIVFHPYWMIFGEVYAYEIDVCANDSTLPTICGPGTWLTPFLQAVYLFVQYIIMVNLLIAFFNNVYLQVKAISNIVWKYQRYHFIMAYHEKPVLPPPL -TEMPL -Equivalence 999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 5ZX5_A||821||1134 Template 5ZX5_A||821||1134 -QUERY DSSDGKNEMEIHIKSKKLPITRKFYAFYHAPIVKFWFNTLAYLGFLMLYTFVVLVKMEQLPSVQEWIVIAYIFTYAIEKVREVFMSEAGKISQKIKVWFSDYFNVSDTIAIISFFVGFGLRFGAKWNYINAYDNHVFVAGRLIYCLNIIFWYVRLLDFLAVNQQAGPYVMMIGKMVANMFYIVVIMALVLLSFGVPRKAILYPHEEPSWSLAKDIVFHPYWMIFGEVYAYEIDVCANDSTLPTICGPGTWLTPFLQAVYLFVQYIIMVNLLIAFFNNVYLQVKAISNIVWKYQRYHFIMAYHEKPVLPPPLIIL -QUERY -TEMPL DSSDGKNEMEIHIKSKKLPITRKFYAFYHAPIVKFWFNTLAYLGFLMLYTFVVLVKMEQLPSVQEWIVIAYIFTYAIEKVREVFMSEAGKISQKIKVWFSDYFNVSDTIAIISFFVGFGLRFGAKWNYINAYDNHVFVAGRLIYCLNIIFWYVRLLDFLAVNQQAGPYVMMIGKMVANMFYIVVIMALVLLSFGVPRKAILYPHEEPSWSLAKDIVFHPYWMIFGEVYAYEIDVCANDSTLPTICGPGTWLTPFLQAVYLFVQYIIMVNLLIAFFNNVYLQVKAISNIVWKYQRYHFIMAYHEKPVLPPPLIIL -TEMPL -Equivalence 99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 5ZX5_A||827||1228 Template 5ZX5_A||827||1228 -QUERY NEMEIHIKSKKLPITRKFYAFYHAPIVKFWFNTLAYLGFLMLYTFVVLVKMEQLPSVQEWIVIAYIFTYAIEKVREVFMSEAGKISQKIKVWFSDYFNVSDTIAIISFFVGFGLRFGAKWNYINAYDNHVFVAGRLIYCLNIIFWYVRLLDFLAVNQQAGPYVMMIGKMVANMFYIVVIMALVLLSFGVPRKAILYPHEEPSWSLAKDIVFHPYWMIFGEVYAYEIDVCANDSTLPTICGPGTWLTPFLQAVYLFVQYIIMVNLLIAFFNNVYLQVKAISNIVWKYQRYHFIMAYHEKPVLPPPLIILSHIVSLFCCVCKRRKKDKTSDGPKLFLTEEDQKKLHDFEEQCVEMYFDEKDDKFNSGSEERIRVTFERVEQMSIQIKEVGDRVNYIKRSLQSLD -QUERY -TEMPL NEMEIHIKSKKLPITRKFYAFYHAPIVKFWFNTLAYLGFLMLYTFVVLVKMEQLPSVQEWIVIAYIFTYAIEKVREVFMSEAGKISQKIKVWFSDYFNVSDTIAIISFFVGFGLRFGAKWNYINAYDNHVFVAGRLIYCLNIIFWYVRLLDFLAVNQQAGPYVMMIGKMVANMFYIVVIMALVLLSFGVPRKAILYPHEEPSWSLAKDIVFHPYWMIFGEVYAYEIDVCANDSTLPTICGPGTWLTPFLQAVYLFVQYIIMVNLLIAFFNNVYLQVKAISNIVWKYQRYHFIMAYHEKPVLPPPLIILSHIVSLFCCVCKRRKKDKTSDGPKLFLTEEDQKKLHDFEEQCVEMYFDEKDDKFNSGSEERIRVTFERVEQMSIQIKEVGDRVNYIKRSLQSLD -TEMPL -Equivalence 999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 6A70_A||27||559 Template 6A70_A||27||559 -QUERY SHPQFEKGSAAAPRVAWAERLVRGLRGLWGTRLMEESSTNREKYLKSVLRELVTYLLFLIVLCILTYGMMSSNVYYYTRMMSQLFLDTPVSKTEKTNFKTLSSMEDFWKFTEGSLLDGLYWKMQPSNQTEADNRSFIFYENLLLGVPRIRQLRVRNGSCSIPQDLRDEIKECYDVYSVSSEDRAPFGPRNGTAWIYTSEKDLNGSSHWGIIATYSGAGYYLDLSRTREETAAQVASLKKNVWLDRGTRATFIDFSVYNANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLIR -QUERY -TEMPL SHPQFEKGSAAAPRVAWAERLVRGLRGLWGTRLMEESSTNREKYLKSVLRELVTYLLFLIVLCILTYGMMSSNVYYYTRMMSQLFLDTPVSKTEKTNFKTLSSMEDFWKFTEGSLLDGLYWKMQPSNQTEADNRSFIFYENLLLGVPRIRQLRVRNGSCSIPQDLRDEIKECYDVYSVSSEDRAPFGPRNGTAWIYTSEKDLNGSSHWGIIATYSGAGYYLDLSRTREETAAQVASLKKNVWLDRGTRATFIDFSVYNANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLIR -TEMPL -Equivalence 99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 6A70_A||284||563 Template 6A70_A||284||563 -QUERY NANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLIRKGYH -QUERY -TEMPL NANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLIRKGYH -TEMPL -Equivalence 9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 6A70_A||39||574 Template 6A70_A||39||574 -QUERY PRVAWAERLVRGLRGLWGTRLMEESSTNREKYLKSVLRELVTYLLFLIVLCILTYGMMSSNVYYYTRMMSQLFLDTPVSKTEKTNFKTLSSMEDFWKFTEGSLLDGLYWKMQPSNQTEADNRSFIFYENLLLGVPRIRQLRVRNGSCSIPQDLRDEIKECYDVYSVSSEDRAPFGPRNGTAWIYTSEKDLNGSSHWGIIATYSGAGYYLDLSRTREETAAQVASLKKNVWLDRGTRATFIDFSVYNANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLIRKGYHKALVKLKLKKN -QUERY -TEMPL PRVAWAERLVRGLRGLWGTRLMEESSTNREKYLKSVLRELVTYLLFLIVLCILTYGMMSSNVYYYTRMMSQLFLDTPVSKTEKTNFKTLSSMEDFWKFTEGSLLDGLYWKMQPSNQTEADNRSFIFYENLLLGVPRIRQLRVRNGSCSIPQDLRDEIKECYDVYSVSSEDRAPFGPRNGTAWIYTSEKDLNGSSHWGIIATYSGAGYYLDLSRTREETAAQVASLKKNVWLDRGTRATFIDFSVYNANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLIRKGYHKALVKLKLKKN -TEMPL -Equivalence 99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 6A70_A||67||562 Template 6A70_A||67||562 -QUERY REKYLKSVLRELVTYLLFLIVLCILTYGMMSSNVYYYTRMMSQLFLDTPVSKTEKTNFKTLSSMEDFWKFTEGSLLDGLYWKMQPSNQTEADNRSFIFYENLLLGVPRIRQLRVRNGSCSIPQDLRDEIKECYDVYSVSSEDRAPFGPRNGTAWIYTSEKDLNGSSHWGIIATYSGAGYYLDLSRTREETAAQVASLKKNVWLDRGTRATFIDFSVYNANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLIRKGY -QUERY -TEMPL REKYLKSVLRELVTYLLFLIVLCILTYGMMSSNVYYYTRMMSQLFLDTPVSKTEKTNFKTLSSMEDFWKFTEGSLLDGLYWKMQPSNQTEADNRSFIFYENLLLGVPRIRQLRVRNGSCSIPQDLRDEIKECYDVYSVSSEDRAPFGPRNGTAWIYTSEKDLNGSSHWGIIATYSGAGYYLDLSRTREETAAQVASLKKNVWLDRGTRATFIDFSVYNANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLIRKGY -TEMPL -Equivalence 9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 6A70_B||227||1129 Template 6A70_B||227||1129 -QUERY LRFRRLLVAELQRGFFDKHIWLSIWDRPPRSRFTRIQRATCCVLLICLFLGANAVWYGAVGDSAYSTGHVSRLSPLSVDTVAVGLVSSVVVYPVYLAILFLFRMSRSKVAGSPSPTPAGQQVLDIDSCLDSSVLDSSFLTFSGLHAEQAFVGQMKSDLFLDDSKSLVCWPSGEGTLSWPDLLSDPSIVGSNLRQLARGQAGHGLGPEEDGFSLASPYSPAKSFSASDEDLIQQVLAEGVSSPAPTQDTHMETDLLSSLSSTPGEKTETLALQRLGELGPPSPGLNWEQPQAARLSRTGLVEGLRKRLLPAWCASLAHGLSLLLVAVAVAVSGWVGASFPPGVSVAWLLSSSASFLASFLGWEPLKVLLEALYFSLVAKRLHPDEDDTLVESPAVTPVSARVPRVRPPHGFALFLAKEEARKVKRLHGMLRSLLVYMLFLLVTLLASYGDASCHGHAYRLQSAIKQELHSRAFLAITRSEELWPWMAHVLLPYVHGNQSSPELGPPRLRQVRLQEALYPDPPGPRVHTCSAAGGFSTSDYDVGWESPHNGSGTWAYSAPDLLGAWSWGSCAVYDSGGYVQELGLSLEESRDRLRFLQLHNWLDNRSRAVFLELTRYSPAVGLHAAVTLRLEFPAAGRALAALSVRPFALRRLSAGLSLPLLTSVCLLLFAVHFAVAEARTWHREGRWRVLRLGAWARWLLVALTAATALVRLAQLGAADRQWTRFVRGRPRRFTSFDQVAQLSSAARGLAASLLFLLLVKAAQQLRFVRQWSVFGKTLCRALPELLGVTLGLVVLGVAYAQLAILLVSSCVDSLWSVAQALLVLCPGTGLSTLCPAESWHLSPLLCVGLWALRLWGALRLGAVILRWRYHALRGELYRPAWEPQDYEMVELFLRRLRLWMGLSK -QUERY -TEMPL LRFRRLLVAELQRGFFDKHIWLSIWDRPPRSRFTRIQRATCCVLLICLFLGANAVWYGAVGDSAYSTGHVSRLSPLSVDTVAVGLVSSVVVYPVYLAILFLFRMSRSKVAGSPSPTPAGQQVLDIDSCLDSSVLDSSFLTFSGLHAEQAFVGQMKSDLFLDDSKSLVCWPSGEGTLSWPDLLSDPSIVGSNLRQLARGQAGHGLGPEEDGFSLASPYSPAKSFSASDEDLIQQVLAEGVSSPAPTQDTHMETDLLSSLSSTPGEKTETLALQRLGELGPPSPGLNWEQPQAARLSRTGLVEGLRKRLLPAWCASLAHGLSLLLVAVAVAVSGWVGASFPPGVSVAWLLSSSASFLASFLGWEPLKVLLEALYFSLVAKRLHPDEDDTLVESPAVTPVSARVPRVRPPHGFALFLAKEEARKVKRLHGMLRSLLVYMLFLLVTLLASYGDASCHGHAYRLQSAIKQELHSRAFLAITRSEELWPWMAHVLLPYVHGNQSSPELGPPRLRQVRLQEALYPDPPGPRVHTCSAAGGFSTSDYDVGWESPHNGSGTWAYSAPDLLGAWSWGSCAVYDSGGYVQELGLSLEESRDRLRFLQLHNWLDNRSRAVFLELTRYSPAVGLHAAVTLRLEFPAAGRALAALSVRPFALRRLSAGLSLPLLTSVCLLLFAVHFAVAEARTWHREGRWRVLRLGAWARWLLVALTAATALVRLAQLGAADRQWTRFVRGRPRRFTSFDQVAQLSSAARGLAASLLFLLLVKAAQQLRFVRQWSVFGKTLCRALPELLGVTLGLVVLGVAYAQLAILLVSSCVDSLWSVAQALLVLCPGTGLSTLCPAESWHLSPLLCVGLWALRLWGALRLGAVILRWRYHALRGELYRPAWEPQDYEMVELFLRRLRLWMGLSK -TEMPL -Equivalence 999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 6AEI_A||287||663 Template 6AEI_A||287||663 -QUERY LAKLKVAIKYHQKEFVAQPNCQQLLATLWYDGFPGWRRKHWVVKLLTCMTIGFLFPMLSIAYLISPRSNLGLFIKKPFIKFICHTASYLTFLFMLLLASQHIVRTDLHVQGPPPTVVEWMILPWVLGFIWGEIKEMWDGGFTEYIHDWWNLMDFAMNSLYLATISLKIVAYVKYNGSRPREEWEMWHPTLIAEALFAISNILSSLRLISLFTANSHLGPLQISLGRMLLDILKFLFIYCLVLLAFANGLNQLYFYYETRAIDEPNNCKGIRCEKQNNAFSTLFETLQSLFWSVFGLLNLYVTNVKARHEFTEFVGATMFGTYNVISLVVLLNMLIAMMNNSYQLIADHADIEWKFARTKLWMSYFDEGGTLPPPFNI -QUERY -TEMPL LAKLKVAIKYHQKEFVAQPNCQQLLATLWYDGFPGWRRKHWVVKLLTCMTIGFLFPMLSIAYLISPRSNLGLFIKKPFIKFICHTASYLTFLFMLLLASQHIVRTDLHVQGPPPTVVEWMILPWVLGFIWGEIKEMWDGGFTEYIHDWWNLMDFAMNSLYLATISLKIVAYVKYNGSRPREEWEMWHPTLIAEALFAISNILSSLRLISLFTANSHLGPLQISLGRMLLDILKFLFIYCLVLLAFANGLNQLYFYYETRAIDEPNNCKGIRCEKQNNAFSTLFETLQSLFWSVFGLLNLYVTNVKARHEFTEFVGATMFGTYNVISLVVLLNMLIAMMNNSYQLIADHADIEWKFARTKLWMSYFDEGGTLPPPFNI -TEMPL -Equivalence 99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 6AEI_A||290||664 Template 6AEI_A||290||664 -QUERY LKVAIKYHQKEFVAQPNCQQLLATLWYDGFPGWRRKHWVVKLLTCMTIGFLFPMLSIAYLISPRSNLGLFIKKPFIKFICHTASYLTFLFMLLLASQHIVRTDLHVQGPPPTVVEWMILPWVLGFIWGEIKEMWDGGFTEYIHDWWNLMDFAMNSLYLATISLKIVAYVKYNGSRPREEWEMWHPTLIAEALFAISNILSSLRLISLFTANSHLGPLQISLGRMLLDILKFLFIYCLVLLAFANGLNQLYFYYETRAIDEPNNCKGIRCEKQNNAFSTLFETLQSLFWSVFGLLNLYVTNVKARHEFTEFVGATMFGTYNVISLVVLLNMLIAMMNNSYQLIADHADIEWKFARTKLWMSYFDEGGTLPPPFNII -QUERY -TEMPL LKVAIKYHQKEFVAQPNCQQLLATLWYDGFPGWRRKHWVVKLLTCMTIGFLFPMLSIAYLISPRSNLGLFIKKPFIKFICHTASYLTFLFMLLLASQHIVRTDLHVQGPPPTVVEWMILPWVLGFIWGEIKEMWDGGFTEYIHDWWNLMDFAMNSLYLATISLKIVAYVKYNGSRPREEWEMWHPTLIAEALFAISNILSSLRLISLFTANSHLGPLQISLGRMLLDILKFLFIYCLVLLAFANGLNQLYFYYETRAIDEPNNCKGIRCEKQNNAFSTLFETLQSLFWSVFGLLNLYVTNVKARHEFTEFVGATMFGTYNVISLVVLLNMLIAMMNNSYQLIADHADIEWKFARTKLWMSYFDEGGTLPPPFNII -TEMPL -Equivalence 999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 6AEI_A||291||667 Template 6AEI_A||291||667 -QUERY KVAIKYHQKEFVAQPNCQQLLATLWYDGFPGWRRKHWVVKLLTCMTIGFLFPMLSIAYLISPRSNLGLFIKKPFIKFICHTASYLTFLFMLLLASQHIVRTDLHVQGPPPTVVEWMILPWVLGFIWGEIKEMWDGGFTEYIHDWWNLMDFAMNSLYLATISLKIVAYVKYNGSRPREEWEMWHPTLIAEALFAISNILSSLRLISLFTANSHLGPLQISLGRMLLDILKFLFIYCLVLLAFANGLNQLYFYYETRAIDEPNNCKGIRCEKQNNAFSTLFETLQSLFWSVFGLLNLYVTNVKARHEFTEFVGATMFGTYNVISLVVLLNMLIAMMNNSYQLIADHADIEWKFARTKLWMSYFDEGGTLPPPFNIIPSP -QUERY -TEMPL KVAIKYHQKEFVAQPNCQQLLATLWYDGFPGWRRKHWVVKLLTCMTIGFLFPMLSIAYLISPRSNLGLFIKKPFIKFICHTASYLTFLFMLLLASQHIVRTDLHVQGPPPTVVEWMILPWVLGFIWGEIKEMWDGGFTEYIHDWWNLMDFAMNSLYLATISLKIVAYVKYNGSRPREEWEMWHPTLIAEALFAISNILSSLRLISLFTANSHLGPLQISLGRMLLDILKFLFIYCLVLLAFANGLNQLYFYYETRAIDEPNNCKGIRCEKQNNAFSTLFETLQSLFWSVFGLLNLYVTNVKARHEFTEFVGATMFGTYNVISLVVLLNMLIAMMNNSYQLIADHADIEWKFARTKLWMSYFDEGGTLPPPFNIIPSP -TEMPL -Equivalence 99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 6AYF_A||19||546 Template 6AYF_A||19||546 -QUERY HEEENRCNFNQQTSPSEELLLEDQMRRKLKFFFMNPCEKFWARGRKPWKLAIQILKIAMVTIQLVLFGLSNQMVVAFKEENTIAFKHLFLKGYMDRMDDTYAVYTQSDVYDQLIFAVNQYLQLYNVSVGNHAYENKGTKQSAMAICQHFYKRGNIYPGNDTFDIDPEIETECFFVEPDEPFHIGTPAENKLNLTLDFHRLLTVELQFKLKAINLQTVRHQELPDCYDFTLTITFDNKAHSGRIKISLDNDISIRECKDWHVSGSIQKNTHYMMIFDAFVILTCLVSLILCIRSVIRGLQLQQEFVNFFLLHYKKEVSVSDQMEFVNGWYIMIIISDILTIIGSILKMEIQAKSLTSYDVCSILLGTSTMLVWLGVIRYLGFFAKYNLLILTLQAALPNVIRFCCCAAMIYLGYCFCGWIVLGPYHDKFRSLNMVSECLFSLINGDDMFATFAKMQQKSYLVWLFSRIYLYSFISLFIYMILSLFIALITDTYETIKQYQQDGFPETELRTFISECKDLPNSGKYRLED -QUERY -TEMPL HEEENRCNFNQQTSPSEELLLEDQMRRKLKFFFMNPCEKFWARGRKPWKLAIQILKIAMVTIQLVLFGLSNQMVVAFKEENTIAFKHLFLKGYMDRMDDTYAVYTQSDVYDQLIFAVNQYLQLYNVSVGNHAYENKGTKQSAMAICQHFYKRGNIYPGNDTFDIDPEIETECFFVEPDEPFHIGTPAENKLNLTLDFHRLLTVELQFKLKAINLQTVRHQELPDCYDFTLTITFDNKAHSGRIKISLDNDISIRECKDWHVSGSIQKNTHYMMIFDAFVILTCLVSLILCIRSVIRGLQLQQEFVNFFLLHYKKEVSVSDQMEFVNGWYIMIIISDILTIIGSILKMEIQAKSLTSYDVCSILLGTSTMLVWLGVIRYLGFFAKYNLLILTLQAALPNVIRFCCCAAMIYLGYCFCGWIVLGPYHDKFRSLNMVSECLFSLINGDDMFATFAKMQQKSYLVWLFSRIYLYSFISLFIYMILSLFIALITDTYETIKQYQQDGFPETELRTFISECKDLPNSGKYRLED -TEMPL -Equivalence 999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 6BBJ_A||424||746 Template 6BBJ_A||424||746 -QUERY GEEVSVLEILVYNSKVENRHEMLAVEPINELLRDKWQKFGAVSFYISVVSYLIAMIIFTLIAYYRPMDGTPPYPYRTTMDYMRLAGEIVTLLTGVVFFITNIKDLFMKKCPGVNSLFIDGSFQLLYFIYSVLVIITAVLYLVGIESYLAVMVFALVLGWMNALYFTRGLKLTGTYSIMLQKILFKDLFRFLLVYLLFMIGYASALVSLLNPCTSQESCIETSSNCTVPEYPSCRDSSTFSKFLLDLFKLTIGMGDLEMINSAKYPAVFIILLVTYIILTFVLLLNMLIALMGETVGQVSKESKQIWKLQWATTILDIERSFPV -QUERY -TEMPL GEEVSVLEILVYNSKVENRHEMLAVEPINELLRDKWQKFGAVSFYISVVSYLIAMIIFTLIAYYRPMDGTPPYPYRTTMDYMRLAGEIVTLLTGVVFFITNIKDLFMKKCPGVNSLFIDGSFQLLYFIYSVLVIITAVLYLVGIESYLAVMVFALVLGWMNALYFTRGLKLTGTYSIMLQKILFKDLFRFLLVYLLFMIGYASALVSLLNPCTSQESCIETSSNCTVPEYPSCRDSSTFSKFLLDLFKLTIGMGDLEMINSAKYPAVFIILLVTYIILTFVLLLNMLIALMGETVGQVSKESKQIWKLQWATTILDIERSFPV -TEMPL -Equivalence 99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 6BBJ_A||428||750 Template 6BBJ_A||428||750 -QUERY SVLEILVYNSKVENRHEMLAVEPINELLRDKWQKFGAVSFYISVVSYLIAMIIFTLIAYYRPMDGTPPYPYRTTMDYMRLAGEIVTLLTGVVFFITNIKDLFMKKCPGVNSLFIDGSFQLLYFIYSVLVIITAVLYLVGIESYLAVMVFALVLGWMNALYFTRGLKLTGTYSIMLQKILFKDLFRFLLVYLLFMIGYASALVSLLNPCTSQESCIETSSNCTVPEYPSCRDSSTFSKFLLDLFKLTIGMGDLEMINSAKYPAVFIILLVTYIILTFVLLLNMLIALMGETVGQVSKESKQIWKLQWATTILDIERSFPVCMRK -QUERY -TEMPL SVLEILVYNSKVENRHEMLAVEPINELLRDKWQKFGAVSFYISVVSYLIAMIIFTLIAYYRPMDGTPPYPYRTTMDYMRLAGEIVTLLTGVVFFITNIKDLFMKKCPGVNSLFIDGSFQLLYFIYSVLVIITAVLYLVGIESYLAVMVFALVLGWMNALYFTRGLKLTGTYSIMLQKILFKDLFRFLLVYLLFMIGYASALVSLLNPCTSQESCIETSSNCTVPEYPSCRDSSTFSKFLLDLFKLTIGMGDLEMINSAKYPAVFIILLVTYIILTFVLLLNMLIALMGETVGQVSKESKQIWKLQWATTILDIERSFPVCMRK -TEMPL -Equivalence 99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 6BCO_A||735||1081 Template 6BCO_A||735||1081 -QUERY PPGTVEPSAKVALERRQRRRPGRALCCGKFSKRWSDFWGAPVTAFLGNVVSYLLFLLLFAHVLLVDFQPTKPSVSELLLYFWAFTLLCEELRQGLGGGWGSLASGGRGPDRAPLRHRLHLYLSDTWNQCDLLALTCFLLGVGCRLTPGLFDLGRTVLCLDFMIFTLRLLHIFTVNKQLGPKIVIVSKMMKDVFFFLFFLCVWLVAYGVATEGILRPQDRSLPSILRRVFYRPYLQIFGQIPQEEMDVALMIPGNCSMERGSWAHPEGPVAGSCVSQYANWLVVLLLIVFLLVANILLLNLLIAMFSYTFSKVHGNSDLYWKAQRYSLIREFHSRPALAPPLIIISHV -QUERY -TEMPL PPGTVEPSAKVALERRQRRRPGRALCCGKFSKRWSDFWGAPVTAFLGNVVSYLLFLLLFAHVLLVDFQPTKPSVSELLLYFWAFTLLCEELRQGLGGGWGSLASGGRGPDRAPLRHRLHLYLSDTWNQCDLLALTCFLLGVGCRLTPGLFDLGRTVLCLDFMIFTLRLLHIFTVNKQLGPKIVIVSKMMKDVFFFLFFLCVWLVAYGVATEGILRPQDRSLPSILRRVFYRPYLQIFGQIPQEEMDVALMIPGNCSMERGSWAHPEGPVAGSCVSQYANWLVVLLLIVFLLVANILLLNLLIAMFSYTFSKVHGNSDLYWKAQRYSLIREFHSRPALAPPLIIISHV -TEMPL -Equivalence 99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 6BO5_A||314||642 Template 6BO5_A||314||642 -QUERY NSVLEIIAFHCKSPNRHRMVVLEPLNKLLQEKWDRLVSRFFFNFACYLVYMFIFTVVAYHQPSLDQPAIPSSKATFGESMLLLGHILILLGGIYLLLGQLWYFWRRRLFIWISFMDSYFEILFLLQALLTVLSQVLRFMETEWYLPLLVLSLVLGWLNLLYYTRGFQHTGIYSVMIQKVILRDLLRFLLVYLVFLFGFAVALVSLSREARSPKAPEDNNSTVTEQPTVGQEEEPAPYRSILDASLELFKFTIGMGELAFQEQLRFRGVVLLLLLAYVLLTYVLLLNMLIALMSETVNHVADNSWSIWKLQKAISVLEMENGYWWCRRKK -QUERY -TEMPL NSVLEIIAFHCKSPNRHRMVVLEPLNKLLQEKWDRLVSRFFFNFACYLVYMFIFTVVAYHQPSLDQPAIPSSKATFGESMLLLGHILILLGGIYLLLGQLWYFWRRRLFIWISFMDSYFEILFLLQALLTVLSQVLRFMETEWYLPLLVLSLVLGWLNLLYYTRGFQHTGIYSVMIQKVILRDLLRFLLVYLVFLFGFAVALVSLSREARSPKAPEDNNSTVTEQPTVGQEEEPAPYRSILDASLELFKFTIGMGELAFQEQLRFRGVVLLLLLAYVLLTYVLLLNMLIALMSETVNHVADNSWSIWKLQKAISVLEMENGYWWCRRKK -TEMPL -Equivalence 99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 6BO8_A||288||614 Template 6BO8_A||288||614 -QUERY DEQSLLELIITTKKREARQILDQTPVKELVSLKWKRYGRPYFCMLGAIYLLYIICFTMCCIYRPLKPRTNNRTSPRDNTLLQQKLLQEAYMTPKDDIRLVGELVTVIGAIIILLVEVPDIFRMGVTRFFGQTILGGPFHVLIITYAFMVLVTMVMRLISASGEVVPMSFALVLGWCNVMYFARGFQMLGPFTIMIQKMIFGDLMRFCWLMAVVILGFASAFYIIFQTEDPEELGHFYDYPMALFSTFELFLTIIDGPANYNVDLPFMYSITYAAFAIIATLLMLNLLIAMMGDTHWRVAHERDELWRAQIVATTVMLERKLPRCLWP -QUERY -TEMPL DEQSLLELIITTKKREARQILDQTPVKELVSLKWKRYGRPYFCMLGAIYLLYIICFTMCCIYRPLKPRTNNRTSPRDNTLLQQKLLQEAYMTPKDDIRLVGELVTVIGAIIILLVEVPDIFRMGVTRFFGQTILGGPFHVLIITYAFMVLVTMVMRLISASGEVVPMSFALVLGWCNVMYFARGFQMLGPFTIMIQKMIFGDLMRFCWLMAVVILGFASAFYIIFQTEDPEELGHFYDYPMALFSTFELFLTIIDGPANYNVDLPFMYSITYAAFAIIATLLMLNLLIAMMGDTHWRVAHERDELWRAQIVATTVMLERKLPRCLWP -TEMPL -Equivalence 999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 6BO8_A||384||609 Template 6BO8_A||384||609 -QUERY IRLVGELVTVIGAIIILLVEVPDIFRMGVTRFFGQTILGGPFHVLIITYAFMVLVTMVMRLISASGEVVPMSFALVLGWCNVMYFARGFQMLGPFTIMIQKMIFGDLMRFCWLMAVVILGFASAFYIIFQTEDPEELGHFYDYPMALFSTFELFLTIIDGPANYNVDLPFMYSITYAAFAIIATLLMLNLLIAMMGDTHWRVAHERDELWRAQIVATTVMLERKLP -QUERY -TEMPL IRLVGELVTVIGAIIILLVEVPDIFRMGVTRFFGQTILGGPFHVLIITYAFMVLVTMVMRLISASGEVVPMSFALVLGWCNVMYFARGFQMLGPFTIMIQKMIFGDLMRFCWLMAVVILGFASAFYIIFQTEDPEELGHFYDYPMALFSTFELFLTIIDGPANYNVDLPFMYSITYAAFAIIATLLMLNLLIAMMGDTHWRVAHERDELWRAQIVATTVMLERKLP -TEMPL -Equivalence 9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 6BPQ_A||570||883 Template 6BPQ_A||570||883 -QUERY IILCLFFFPLIGCGFISFRKKPVEKTKKLFLYYVSFFTSPFVVFSWNVIFYIAFLLLFAYVLLMDFQKEPTALEIILYVLVFILLCDEVRQWYMNGSKYFSDLWNVMDTLAIFYFIAGIVFRLHSDESSWYSGRVIFCLDYIVFTLRLIHIFTVSRNLGPKIIMLQRMMIDVFFFLFLFAVWMVAFGVARQGILRKNEHRWEWIFRSVIYEPYLAMFGQYPDDIDGTTYNFDHCTFSGNESKPLCVELDANNQPRFPEWITIPLVCIYMLSTNILLVNLLVAMFGYTVGSVQENNDQVWKFQRFFLVQEYCSRL -QUERY -TEMPL IILCLFFFPLIGCGFISFRKKPVEKTKKLFLYYVSFFTSPFVVFSWNVIFYIAFLLLFAYVLLMDFQKEPTALEIILYVLVFILLCDEVRQWYMNGSKYFSDLWNVMDTLAIFYFIAGIVFRLHSDESSWYSGRVIFCLDYIVFTLRLIHIFTVSRNLGPKIIMLQRMMIDVFFFLFLFAVWMVAFGVARQGILRKNEHRWEWIFRSVIYEPYLAMFGQYPDDIDGTTYNFDHCTFSGNESKPLCVELDANNQPRFPEWITIPLVCIYMLSTNILLVNLLVAMFGYTVGSVQENNDQVWKFQRFFLVQEYCSRL -TEMPL -Equivalence 99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 6BQR_A||661||1011 Template 6BQR_A||661||1011 -QUERY PVGTADPAEKTPLGVPRQSGRPGCCGGRCGGRRCLRRWFHFWGAPVTIFMGNVVSYLLFLLLFSRVLLVDFQPAPPGSLELLLYFWAFTLLCEELRQGLSGGGGSLASGGPGPGHASLSQRLRLYLADSWNQCDLVALTCFLLGVGCRLTPGLYHLGRTVLCIDFMVFTVRLLHIFTVNKQLGPKIVIVSKMMKDVFFFLFFLGVWLVAYGVATEGLLRPRDSDFPSILRRVFYRPYLQIFGQIPQEDMDVALMEHSNCSSEPGFWAHPPGAQAGTCVSQYANWLVVLLLVIFLLVANILLVNLLIAMFSYTFGKVQGNSDLYWKAQRYRLIREFHSRPALAPPFIVISHL -QUERY -TEMPL PVGTADPAEKTPLGVPRQSGRPGCCGGRCGGRRCLRRWFHFWGAPVTIFMGNVVSYLLFLLLFSRVLLVDFQPAPPGSLELLLYFWAFTLLCEELRQGLSGGGGSLASGGPGPGHASLSQRLRLYLADSWNQCDLVALTCFLLGVGCRLTPGLYHLGRTVLCIDFMVFTVRLLHIFTVNKQLGPKIVIVSKMMKDVFFFLFFLGVWLVAYGVATEGLLRPRDSDFPSILRRVFYRPYLQIFGQIPQEDMDVALMEHSNCSSEPGFWAHPPGAQAGTCVSQYANWLVVLLLVIFLLVANILLVNLLIAMFSYTFGKVQGNSDLYWKAQRYRLIREFHSRPALAPPFIVISHL -TEMPL -Equivalence 999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 6BQV_A||739||1089 Template 6BQV_A||739||1089 -QUERY PVGTADPAEKTPLGVPRQSGRPGCCGGRCGGRRCLRRWFHFWGAPVTIFMGNVVSYLLFLLLFSRVLLVDFQPAPPGSLELLLYFWAFTLLCEELRQGLSGGGGSLASGGPGPGHASLSQRLRLYLADSWNQCDLVALTCFLLGVGCRLTPGLYHLGRTVLCIDFMVFTVRLLHIFTVNKQLGPKIVIVSKMMKDVFFFLFFLGVWLVAYGVATEGLLRPRDSDFPSILRRVFYRPYLQIFGQIPQEDMDVALMEHSNCSSEPGFWAHPPGAQAGTCVSQYANWLVVLLLVIFLLVANILLVNLLIAMFSYTFGKVQGNSDLYWKAQRYRLIREFHSRPALAPPFIVISHL -QUERY -TEMPL PVGTADPAEKTPLGVPRQSGRPGCCGGRCGGRRCLRRWFHFWGAPVTIFMGNVVSYLLFLLLFSRVLLVDFQPAPPGSLELLLYFWAFTLLCEELRQGLSGGGGSLASGGPGPGHASLSQRLRLYLADSWNQCDLVALTCFLLGVGCRLTPGLYHLGRTVLCIDFMVFTVRLLHIFTVNKQLGPKIVIVSKMMKDVFFFLFFLGVWLVAYGVATEGLLRPRDSDFPSILRRVFYRPYLQIFGQIPQEDMDVALMEHSNCSSEPGFWAHPPGAQAGTCVSQYANWLVVLLLVIFLLVANILLVNLLIAMFSYTFGKVQGNSDLYWKAQRYRLIREFHSRPALAPPFIVISHL -TEMPL -Equivalence 999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 6BWD_A||470||712 Template 6BWD_A||470||712 -QUERY FKEVKILDSSDGKNEMEIHIKSKKLPITRKFYAFYHAPIVKFWFNTLAYLGFLMLYTFVVLVKMEQLPSVQEWIVIAYIFTYAIEKVREVFMSEAGKISQKIKVWFSDYFNVSDTIAIISFFVGFGLRFGAKWNYINAYDNHVFVAGRLIYCLNIIFWYVRLLDFLAVNQQAGPYVMMIGKMVANMFYIVVIMALVLLSFGVPRKAILYPHEEPSWSLAKDIVFHPYWMIFGEVYAYEIDVCA -QUERY -TEMPL FKEVKILDSSDGKNEMEIHIKSKKLPITRKFYAFYHAPIVKFWFNTLAYLGFLMLYTFVVLVKMEQLPSVQEWIVIAYIFTYAIEKVREVFMSEAGKISQKIKVWFSDYFNVSDTIAIISFFVGFGLRFGAKWNYINAYDNHVFVAGRLIYCLNIIFWYVRLLDFLAVNQQAGPYVMMIGKMVANMFYIVVIMALVLLSFGVPRKAILYPHEEPSWSLAKDIVFHPYWMIFGEVYAYEIDVCA -TEMPL -Equivalence 999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 6BWD_A||476||787 Template 6BWD_A||476||787 -QUERY LDSSDGKNEMEIHIKSKKLPITRKFYAFYHAPIVKFWFNTLAYLGFLMLYTFVVLVKMEQLPSVQEWIVIAYIFTYAIEKVREVFMSEAGKISQKIKVWFSDYFNVSDTIAIISFFVGFGLRFGAKWNYINAYDNHVFVAGRLIYCLNIIFWYVRLLDFLAVNQQAGPYVMMIGKMVANMFYIVVIMALVLLSFGVPRKAILYPHEEPSWSLAKDIVFHPYWMIFGEVYAYEIDVCANDSTLPTICGPGTWLTPFLQAVYLFVQYIIMVNLLIAFFNNVYLQVKAISNIVWKYQRYHFIMAYHEKPVLPPPL -QUERY -TEMPL LDSSDGKNEMEIHIKSKKLPITRKFYAFYHAPIVKFWFNTLAYLGFLMLYTFVVLVKMEQLPSVQEWIVIAYIFTYAIEKVREVFMSEAGKISQKIKVWFSDYFNVSDTIAIISFFVGFGLRFGAKWNYINAYDNHVFVAGRLIYCLNIIFWYVRLLDFLAVNQQAGPYVMMIGKMVANMFYIVVIMALVLLSFGVPRKAILYPHEEPSWSLAKDIVFHPYWMIFGEVYAYEIDVCANDSTLPTICGPGTWLTPFLQAVYLFVQYIIMVNLLIAFFNNVYLQVKAISNIVWKYQRYHFIMAYHEKPVLPPPL -TEMPL -Equivalence 999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 6BWD_A||477||790 Template 6BWD_A||477||790 -QUERY DSSDGKNEMEIHIKSKKLPITRKFYAFYHAPIVKFWFNTLAYLGFLMLYTFVVLVKMEQLPSVQEWIVIAYIFTYAIEKVREVFMSEAGKISQKIKVWFSDYFNVSDTIAIISFFVGFGLRFGAKWNYINAYDNHVFVAGRLIYCLNIIFWYVRLLDFLAVNQQAGPYVMMIGKMVANMFYIVVIMALVLLSFGVPRKAILYPHEEPSWSLAKDIVFHPYWMIFGEVYAYEIDVCANDSTLPTICGPGTWLTPFLQAVYLFVQYIIMVNLLIAFFNNVYLQVKAISNIVWKYQRYHFIMAYHEKPVLPPPLIIL -QUERY -TEMPL DSSDGKNEMEIHIKSKKLPITRKFYAFYHAPIVKFWFNTLAYLGFLMLYTFVVLVKMEQLPSVQEWIVIAYIFTYAIEKVREVFMSEAGKISQKIKVWFSDYFNVSDTIAIISFFVGFGLRFGAKWNYINAYDNHVFVAGRLIYCLNIIFWYVRLLDFLAVNQQAGPYVMMIGKMVANMFYIVVIMALVLLSFGVPRKAILYPHEEPSWSLAKDIVFHPYWMIFGEVYAYEIDVCANDSTLPTICGPGTWLTPFLQAVYLFVQYIIMVNLLIAFFNNVYLQVKAISNIVWKYQRYHFIMAYHEKPVLPPPLIIL -TEMPL -Equivalence 99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 6BWD_A||480||793 Template 6BWD_A||480||793 -QUERY DGKNEMEIHIKSKKLPITRKFYAFYHAPIVKFWFNTLAYLGFLMLYTFVVLVKMEQLPSVQEWIVIAYIFTYAIEKVREVFMSEAGKISQKIKVWFSDYFNVSDTIAIISFFVGFGLRFGAKWNYINAYDNHVFVAGRLIYCLNIIFWYVRLLDFLAVNQQAGPYVMMIGKMVANMFYIVVIMALVLLSFGVPRKAILYPHEEPSWSLAKDIVFHPYWMIFGEVYAYEIDVCANDSTLPTICGPGTWLTPFLQAVYLFVQYIIMVNLLIAFFNNVYLQVKAISNIVWKYQRYHFIMAYHEKPVLPPPLIILSHI -QUERY -TEMPL DGKNEMEIHIKSKKLPITRKFYAFYHAPIVKFWFNTLAYLGFLMLYTFVVLVKMEQLPSVQEWIVIAYIFTYAIEKVREVFMSEAGKISQKIKVWFSDYFNVSDTIAIISFFVGFGLRFGAKWNYINAYDNHVFVAGRLIYCLNIIFWYVRLLDFLAVNQQAGPYVMMIGKMVANMFYIVVIMALVLLSFGVPRKAILYPHEEPSWSLAKDIVFHPYWMIFGEVYAYEIDVCANDSTLPTICGPGTWLTPFLQAVYLFVQYIIMVNLLIAFFNNVYLQVKAISNIVWKYQRYHFIMAYHEKPVLPPPLIILSHI -TEMPL -Equivalence 99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 6BWD_A||483||904 Template 6BWD_A||483||904 -QUERY NEMEIHIKSKKLPITRKFYAFYHAPIVKFWFNTLAYLGFLMLYTFVVLVKMEQLPSVQEWIVIAYIFTYAIEKVREVFMSEAGKISQKIKVWFSDYFNVSDTIAIISFFVGFGLRFGAKWNYINAYDNHVFVAGRLIYCLNIIFWYVRLLDFLAVNQQAGPYVMMIGKMVANMFYIVVIMALVLLSFGVPRKAILYPHEEPSWSLAKDIVFHPYWMIFGEVYAYEIDVCANDSTLPTICGPGTWLTPFLQAVYLFVQYIIMVNLLIAFFNNVYLQVKAISNIVWKYQRYHFIMAYHEKPVLPPPLIILSHIVSLFCCVCKRRKKDKTSDGPKLFLTEEDQKKLHDFEEQCVEMYFDEKDDKFNSGSEERIRVTFERVEQMSIQIKEVGDRVNYIKRSLQSLDSQIGHLQDLSALTVDTLKTL -QUERY -TEMPL NEMEIHIKSKKLPITRKFYAFYHAPIVKFWFNTLAYLGFLMLYTFVVLVKMEQLPSVQEWIVIAYIFTYAIEKVREVFMSEAGKISQKIKVWFSDYFNVSDTIAIISFFVGFGLRFGAKWNYINAYDNHVFVAGRLIYCLNIIFWYVRLLDFLAVNQQAGPYVMMIGKMVANMFYIVVIMALVLLSFGVPRKAILYPHEEPSWSLAKDIVFHPYWMIFGEVYAYEIDVCANDSTLPTICGPGTWLTPFLQAVYLFVQYIIMVNLLIAFFNNVYLQVKAISNIVWKYQRYHFIMAYHEKPVLPPPLIILSHIVSLFCCVCKRRKKDKTSDGPKLFLTEEDQKKLHDFEEQCVEMYFDEKDDKFNSGSEERIRVTFERVEQMSIQIKEVGDRVNYIKRSLQSLDSQIGHLQDLSALTVDTLKTL -TEMPL -Equivalence 99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 6BWI_A||536||886 Template 6BWI_A||536||886 -QUERY PVGTADPAEKTPLGVPRQSGRPGCCGGRCGGRRCLRRWFHFWGAPVTIFMGNVVSYLLFLLLFSRVLLVDFQPAPPGSLELLLYFWAFTLLCEELRQGLSGGGGSLASGGPGPGHASLSQRLRLYLADSWNQCDLVALTCFLLGVGCRLTPGLYHLGRTVLCIDFMVFTVRLLHIFTVNKQLGPKIVIVSKMMKDVFFFLFFLGVWLVAYGVATEGLLRPRDSDFPSILRRVFYRPYLQIFGQIPQEDMDVALMEHSNCSSEPGFWAHPPGAQAGTCVSQYANWLVVLLLVIFLLVANILLVNLLIAMFSYTFGKVQGNSDLYWKAQRYRLIREFHSRPALAPPFIVISHL -QUERY -TEMPL PVGTADPAEKTPLGVPRQSGRPGCCGGRCGGRRCLRRWFHFWGAPVTIFMGNVVSYLLFLLLFSRVLLVDFQPAPPGSLELLLYFWAFTLLCEELRQGLSGGGGSLASGGPGPGHASLSQRLRLYLADSWNQCDLVALTCFLLGVGCRLTPGLYHLGRTVLCIDFMVFTVRLLHIFTVNKQLGPKIVIVSKMMKDVFFFLFFLGVWLVAYGVATEGLLRPRDSDFPSILRRVFYRPYLQIFGQIPQEDMDVALMEHSNCSSEPGFWAHPPGAQAGTCVSQYANWLVVLLLVIFLLVANILLVNLLIAMFSYTFGKVQGNSDLYWKAQRYRLIREFHSRPALAPPFIVISHL -TEMPL -Equivalence 999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 6BWJ_A||351||680 Template 6BWJ_A||351||680 -QUERY NSVLEIIAFHSRSPHRHRMVVLEPLNKLLQAKWDRLIPRFCFNFLCYLVYMLIFTAVAYHQPALEKQGFPPLKATAGNSMLLLGHILILLGGVYLLLGQLWYFWRRRLFIWISFMDSYSEILFLLQALLTVLSQVLCFLAIEWYLPLLVSSLVMGWTNLLYYTRGFQHTGIYSVMIEKVILRDLLRFLLVYLVFLFGFAVALVSLSREAQNSRTPAGPNATEVGQPGAGQEDEAPPYRSILDASLELFKFTIGMGELAFQEQLRFRGVVLLLLLAYVLLTYVLLLNMLIALMSETVNSVATDSWSIWKLQKAISVLEMENGYWWCRRKKQ -QUERY -TEMPL NSVLEIIAFHSRSPHRHRMVVLEPLNKLLQAKWDRLIPRFCFNFLCYLVYMLIFTAVAYHQPALEKQGFPPLKATAGNSMLLLGHILILLGGVYLLLGQLWYFWRRRLFIWISFMDSYSEILFLLQALLTVLSQVLCFLAIEWYLPLLVSSLVMGWTNLLYYTRGFQHTGIYSVMIEKVILRDLLRFLLVYLVFLFGFAVALVSLSREAQNSRTPAGPNATEVGQPGAGQEDEAPPYRSILDASLELFKFTIGMGELAFQEQLRFRGVVLLLLLAYVLLTYVLLLNMLIALMSETVNSVATDSWSIWKLQKAISVLEMENGYWWCRRKKQ -TEMPL -Equivalence 999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 6C8G_A||293||615 Template 6C8G_A||293||615 -QUERY GEEVSVLEILVYNSKVENRHEMLAVEPINELLRDKWQKFGAVSFYISVVSYLIAMIIFTLIAYYRPMDGTPPYPYRTTMDYMRLAGEIVTLLTGVVFFITNIKDLFMKKCPGVNSLFIDGSFQLLYFIYSVLVIITAVLYLVGIESYLAVMVFALVLGWMNALYFTRGLKLTGTYSIMLQKILFKDLFRFLLVYLLFMIGYASALVSLLNPCTSQESCIETSSQCTVPEYPSCRDSSTFSKFLLDLFKLTIGMGDLEMINSAKYPAVFIILLVTYIILTFVLLLNMLIALMGETVGQVSKESKQIWKLQWATTILDIERSFPV -QUERY -TEMPL GEEVSVLEILVYNSKVENRHEMLAVEPINELLRDKWQKFGAVSFYISVVSYLIAMIIFTLIAYYRPMDGTPPYPYRTTMDYMRLAGEIVTLLTGVVFFITNIKDLFMKKCPGVNSLFIDGSFQLLYFIYSVLVIITAVLYLVGIESYLAVMVFALVLGWMNALYFTRGLKLTGTYSIMLQKILFKDLFRFLLVYLLFMIGYASALVSLLNPCTSQESCIETSSQCTVPEYPSCRDSSTFSKFLLDLFKLTIGMGDLEMINSAKYPAVFIILLVTYIILTFVLLLNMLIALMGETVGQVSKESKQIWKLQWATTILDIERSFPV -TEMPL -Equivalence 99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 6C8G_A||294||617 Template 6C8G_A||294||617 -QUERY EEVSVLEILVYNSKVENRHEMLAVEPINELLRDKWQKFGAVSFYISVVSYLIAMIIFTLIAYYRPMDGTPPYPYRTTMDYMRLAGEIVTLLTGVVFFITNIKDLFMKKCPGVNSLFIDGSFQLLYFIYSVLVIITAVLYLVGIESYLAVMVFALVLGWMNALYFTRGLKLTGTYSIMLQKILFKDLFRFLLVYLLFMIGYASALVSLLNPCTSQESCIETSSQCTVPEYPSCRDSSTFSKFLLDLFKLTIGMGDLEMINSAKYPAVFIILLVTYIILTFVLLLNMLIALMGETVGQVSKESKQIWKLQWATTILDIERSFPVCM -QUERY -TEMPL EEVSVLEILVYNSKVENRHEMLAVEPINELLRDKWQKFGAVSFYISVVSYLIAMIIFTLIAYYRPMDGTPPYPYRTTMDYMRLAGEIVTLLTGVVFFITNIKDLFMKKCPGVNSLFIDGSFQLLYFIYSVLVIITAVLYLVGIESYLAVMVFALVLGWMNALYFTRGLKLTGTYSIMLQKILFKDLFRFLLVYLLFMIGYASALVSLLNPCTSQESCIETSSQCTVPEYPSCRDSSTFSKFLLDLFKLTIGMGDLEMINSAKYPAVFIILLVTYIILTFVLLLNMLIALMGETVGQVSKESKQIWKLQWATTILDIERSFPVCM -TEMPL -Equivalence 999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 6C8G_A||295||619 Template 6C8G_A||295||619 -QUERY EVSVLEILVYNSKVENRHEMLAVEPINELLRDKWQKFGAVSFYISVVSYLIAMIIFTLIAYYRPMDGTPPYPYRTTMDYMRLAGEIVTLLTGVVFFITNIKDLFMKKCPGVNSLFIDGSFQLLYFIYSVLVIITAVLYLVGIESYLAVMVFALVLGWMNALYFTRGLKLTGTYSIMLQKILFKDLFRFLLVYLLFMIGYASALVSLLNPCTSQESCIETSSQCTVPEYPSCRDSSTFSKFLLDLFKLTIGMGDLEMINSAKYPAVFIILLVTYIILTFVLLLNMLIALMGETVGQVSKESKQIWKLQWATTILDIERSFPVCMRK -QUERY -TEMPL EVSVLEILVYNSKVENRHEMLAVEPINELLRDKWQKFGAVSFYISVVSYLIAMIIFTLIAYYRPMDGTPPYPYRTTMDYMRLAGEIVTLLTGVVFFITNIKDLFMKKCPGVNSLFIDGSFQLLYFIYSVLVIITAVLYLVGIESYLAVMVFALVLGWMNALYFTRGLKLTGTYSIMLQKILFKDLFRFLLVYLLFMIGYASALVSLLNPCTSQESCIETSSQCTVPEYPSCRDSSTFSKFLLDLFKLTIGMGDLEMINSAKYPAVFIILLVTYIILTFVLLLNMLIALMGETVGQVSKESKQIWKLQWATTILDIERSFPVCMRK -TEMPL -Equivalence 9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 6C8G_A||419||661 Template 6C8G_A||419||661 -QUERY FIYSVLVIITAVLYLVGIESYLAVMVFALVLGWMNALYFTRGLKLTGTYSIMLQKILFKDLFRFLLVYLLFMIGYASALVSLLNPCTSQESCIETSSQCTVPEYPSCRDSSTFSKFLLDLFKLTIGMGDLEMINSAKYPAVFIILLVTYIILTFVLLLNMLIALMGETVGQVSKESKQIWKLQWATTILDIERSFPVCMRKAFRSGEMVTVGKNLDGTPDRRWCFRVDEVNWSHWNQNLGIIN -QUERY -TEMPL FIYSVLVIITAVLYLVGIESYLAVMVFALVLGWMNALYFTRGLKLTGTYSIMLQKILFKDLFRFLLVYLLFMIGYASALVSLLNPCTSQESCIETSSQCTVPEYPSCRDSSTFSKFLLDLFKLTIGMGDLEMINSAKYPAVFIILLVTYIILTFVLLLNMLIALMGETVGQVSKESKQIWKLQWATTILDIERSFPVCMRKAFRSGEMVTVGKNLDGTPDRRWCFRVDEVNWSHWNQNLGIIN -TEMPL -Equivalence 999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 6CO7_A||808||1043 Template 6CO7_A||808||1043 -QUERY EIREDDSMEVIMRNKKLGFCDRIMHFYSAPFSKFVGNVVGYLAFIFLYAYVVLFNFPRFDPAKTLGGIHPTEIVLYFWVFTILIEEIRQLAAKPPKYIKDKVSVYFSDTWNFVDIFSLTVFIIAIILRFFTNSRIFTASRIILSLDIIFFIVRSLQIFSVNRLLGPKLVMIQKMMQDLAQFIIILAVFTIAYGIALHAVMFPSPGIYARNNTWVTITSVVQYPYWQMYGELFLDEI -QUERY -TEMPL EIREDDSMEVIMRNKKLGFCDRIMHFYSAPFSKFVGNVVGYLAFIFLYAYVVLFNFPRFDPAKTLGGIHPTEIVLYFWVFTILIEEIRQLAAKPPKYIKDKVSVYFSDTWNFVDIFSLTVFIIAIILRFFTNSRIFTASRIILSLDIIFFIVRSLQIFSVNRLLGPKLVMIQKMMQDLAQFIIILAVFTIAYGIALHAVMFPSPGIYARNNTWVTITSVVQYPYWQMYGELFLDEI -TEMPL -Equivalence 99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - -Query 6CO7_A||810||1124 Template 6CO7_A||810||1124 -QUERY REDDSMEVIMRNKKLGFCDRIMHFYSAPFSKFVGNVVGYLAFIFLYAYVVLFNFPRFDPAKTLGGIHPTEIVLYFWVFTILIEEIRQLAAKPPKYIKDKVSVYFSDTWNFVDIFSLTVFIIAIILRFFTNSRIFTASRIILSLDIIFFIVRSLQIFSVNRLLGPKLVMIQKMMQDLAQFIIILAVFTIAYGIALHAVMFPSPGIYARNNTWVTITSVVQYPYWQMYGELFLDEIQGEKPKEFGEVDPDGRWLSPLLLAIYMVFTNILLLNLLIAIFNYTFERVQEDSDKVWKFQRYDLVQEYHSRPVFAPPLVLL -QUERY -TEMPL REDDSMEVIMRNKKLGFCDRIMHFYSAPFSKFVGNVVGYLAFIFLYAYVVLFNFPRFDPAKTLGGIHPTEIVLYFWVFTILIEEIRQLAAKPPKYIKDKVSVYFSDTWNFVDIFSLTVFIIAIILRFFTNSRIFTASRIILSLDIIFFIVRSLQIFSVNRLLGPKLVMIQKMMQDLAQFIIILAVFTIAYGIALHAVMFPSPGIYARNNTWVTITSVVQYPYWQMYGELFLDEIQGEKPKEFGEVDPDGRWLSPLLLAIYMVFTNILLLNLLIAIFNYTFERVQEDSDKVWKFQRYDLVQEYHSRPVFAPPLVLL -TEMPL -Equivalence 999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 - diff --git a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/dash_client b/aphylogeo/bin/mafft-linux64/mafftdir/libexec/dash_client deleted file mode 100755 index e30f683e..00000000 Binary files a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/dash_client and /dev/null differ diff --git a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/dash_sequences.fa b/aphylogeo/bin/mafft-linux64/mafftdir/libexec/dash_sequences.fa deleted file mode 100644 index bec30a1e..00000000 --- a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/dash_sequences.fa +++ /dev/null @@ -1,138 +0,0 @@ ->DASH_3J5P_A||281||579 -EKNSVLEVIAYSSSETPNRHDMLLVEPLNRLLQDKWDRFVKRIFYFNFFVYCLYMIIFTAAAYYRPVEGLPPYKLKNTVGDYFRVTGEILSVSGGVYFFFRGIQYFLQRRPSLKSLFVDSYSEILFFVQSLFMLVSVVLYFSQRKEYVASMVFSLAMGWTNMLYYTRGFQQMGIYAVMIEKMILRDLCRFMFVYLVFLFGFSTAVVTLIEDGKYNSLYSTCLELFKFTIGMGDLEFTENYDFKAVFIILLLAYVILTYILLLNMLIALMGETVNKIAQESKNIWKLQRAITILDTEKSF ->DASH_3J5P_A||283||585 -NSVLEVIAYSSSETPNRHDMLLVEPLNRLLQDKWDRFVKRIFYFNFFVYCLYMIIFTAAAYYRPVEGLPPYKLKNTVGDYFRVTGEILSVSGGVYFFFRGIQYFLQRRPSLKSLFVDSYSEILFFVQSLFMLVSVVLYFSQRKEYVASMVFSLAMGWTNMLYYTRGFQQMGIYAVMIEKMILRDLCRFMFVYLVFLFGFSTAVVTLIEDGKYNSLYSTCLELFKFTIGMGDLEFTENYDFKAVFIILLLAYVILTYILLLNMLIALMGETVNKIAQESKNIWKLQRAITILDTEKSFLKCMRK ->DASH_3J9P_A||1089||1399 -YEPLTALNAMVQNNRIELLNHPVCKEYLLMKWLAYGFRAHMMNLGSYCLGLIPMTILVVNIKPGMAFNSTGIINETSDHSEILDTTNSYLIKTCMILVFLSSIFGYCKEAGQIFQQKRNYFMDISNVLEWIIYTTGIIFVLPLFVEIPAHLQWQCGAIAVYFYWMNFLLYLQRFENCGIFIVMLEVILKTLLRSTVVFIFLLLAFGLSFYILLNLQDPFSSPLLSIIQTFSMMLGDINYRESFLEPYLRNELAHPVLSFAQLVSFTIFVPIVLMNLLIGLAVGDIADVQKHASLKRIAMQVELHTSLEKKL ->DASH_3J9P_A||1091||1408 -PLTALNAMVQNNRIELLNHPVCKEYLLMKWLAYGFRAHMMNLGSYCLGLIPMTILVVNIKPGMAFNSTGIINETSDHSEILDTTNSYLIKTCMILVFLSSIFGYCKEAGQIFQQKRNYFMDISNVLEWIIYTTGIIFVLPLFVEIPAHLQWQCGAIAVYFYWMNFLLYLQRFENCGIFIVMLEVILKTLLRSTVVFIFLLLAFGLSFYILLNLQDPFSSPLLSIIQTFSMMLGDINYRESFLEPYLRNELAHPVLSFAQLVSFTIFVPIVLMNLLIGLAVGDIADVQKHASLKRIAMQVELHTSLEKKLPLWFLRKVD ->DASH_3J9P_A||1092||1402 -LTALNAMVQNNRIELLNHPVCKEYLLMKWLAYGFRAHMMNLGSYCLGLIPMTILVVNIKPGMAFNSTGIINETSDHSEILDTTNSYLIKTCMILVFLSSIFGYCKEAGQIFQQKRNYFMDISNVLEWIIYTTGIIFVLPLFVEIPAHLQWQCGAIAVYFYWMNFLLYLQRFENCGIFIVMLEVILKTLLRSTVVFIFLLLAFGLSFYILLNLQDPFSSPLLSIIQTFSMMLGDINYRESFLEPYLRNELAHPVLSFAQLVSFTIFVPIVLMNLLIGLAVGDIADVQKHASLKRIAMQVELHTSLEKKLPLW ->DASH_3J9P_A||1096||1410 -NAMVQNNRIELLNHPVCKEYLLMKWLAYGFRAHMMNLGSYCLGLIPMTILVVNIKPGMAFNSTGIINETSDHSEILDTTNSYLIKTCMILVFLSSIFGYCKEAGQIFQQKRNYFMDISNVLEWIIYTTGIIFVLPLFVEIPAHLQWQCGAIAVYFYWMNFLLYLQRFENCGIFIVMLEVILKTLLRSTVVFIFLLLAFGLSFYILLNLQDPFSSPLLSIIQTFSMMLGDINYRESFLEPYLRNELAHPVLSFAQLVSFTIFVPIVLMNLLIGLAVGDIADVQKHASLKRIAMQVELHTSLEKKLPLWFLRKVDQK ->DASH_5AN8_A||277||586 -NSVLEIIAFHSRSPHRHRMVVLEPLNKLLQAKWDRLIPRFCFNFLCYLVYMLIFTAVAYHQPALEKQGFPPLKATAGNSMLLLGHILILLGGVYLLLGQLWYFWRRRLFIWISFMDSYFEILFLLQALLTVLSQVLCFLAIEWYLPLLVSSLVLGWLNLLYYTRGFQHTGIYSVMIQKVILRDLLRFLLVYLVFLFGFAVALVSLSREAQEDEAPPYRSILDASLELFKFTIGMGELAFQEQLRFRGVVLLLLLAYVLLTYVLLLNMLIALMSETVNSVATDSWSIWKLQKAISVLEMENGYWWCRRKKQ ->DASH_5IRX_A||286||584 -EKNSVLEVIAYSSSETPNRHDMLLVEPLNRLLQDKWDRFVKRIFYFNFFVYCLYMIIFTAAAYYRPVEGLPPYKLKNTVGDYFRVTGEILSVSGGVYFFFRGIQYFLQRRPSLKSLFVDSYSEILFFVQSLFMLVSVVLYFSQRKEYVASMVFSLAMGWTNMLYYTRGFQQMGIYAVMIEKMILRDLCRFMFVYLVFLFGFSTAVVTLIEDGKYNSLYSTCLELFKFTIGMGDLEFTENYDFKAVFIILLLAYVILTYILLLNMLIALMGETVNKIAQESKNIWKLQRAITILDTEKSF ->DASH_5IRX_A||288||590 -NSVLEVIAYSSSETPNRHDMLLVEPLNRLLQDKWDRFVKRIFYFNFFVYCLYMIIFTAAAYYRPVEGLPPYKLKNTVGDYFRVTGEILSVSGGVYFFFRGIQYFLQRRPSLKSLFVDSYSEILFFVQSLFMLVSVVLYFSQRKEYVASMVFSLAMGWTNMLYYTRGFQQMGIYAVMIEKMILRDLCRFMFVYLVFLFGFSTAVVTLIEDGKYNSLYSTCLELFKFTIGMGDLEFTENYDFKAVFIILLLAYVILTYILLLNMLIALMGETVNKIAQESKNIWKLQRAITILDTEKSFLKCMRK ->DASH_5IWK_A||287||613 -DDQSLLELIVTTKKREARQILDQTPVKELVSLKWKRYGRPYFCVLGAIYVLYIICFTMCCVYRPLKPRITNRTNPRDNTLLQQKLLQEAYVTPKDDLRLVGELVSIVGAVIILLVEIPDIFRLGVTRFFGQTILGGPFHVIIVTYAFMVLVTMVMRLTNSDGEVVPMSFALVLGWCNVMYFARGFQMLGPFTIMIQKMIFGDLMRFCWQMAVVILGFASAFYIIFQTEDPDELGHFYDYPMALFSTFELFLTIIDGPANYDVDLPFMYSITYAAFAIIATLLMLNLLIAMMGDTHWRVAHERDELWRAQVVATTVMLERKLPRCLWP ->DASH_5IWK_A||383||608 -LRLVGELVSIVGAVIILLVEIPDIFRLGVTRFFGQTILGGPFHVIIVTYAFMVLVTMVMRLTNSDGEVVPMSFALVLGWCNVMYFARGFQMLGPFTIMIQKMIFGDLMRFCWQMAVVILGFASAFYIIFQTEDPDELGHFYDYPMALFSTFELFLTIIDGPANYDVDLPFMYSITYAAFAIIATLLMLNLLIAMMGDTHWRVAHERDELWRAQVVATTVMLERKLP ->DASH_5K47_A||19||514 -GTRLMEESSTNREKYLKSVLRELVTYLLFLIVLCILTYGMMSSNVYYYTRMMSQLFLDTPVSKTEKTNFKTLSSMEDFWKFTEGSLLDGLYWKMQPSNQTEADNRSFIFYENLLLGVPRIRQLRVRNGSCSIPQDLRDEIKECYDVYSVSSEDRAPFGPRNGTAWIYTSEKDLNGSSHWGIIATYSGAGYYLDLSRTREETAAQVASLKKNVWLDRGTRATFIDFSVYNANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAE ->DASH_5K47_A||20||521 -TRLMEESSTNREKYLKSVLRELVTYLLFLIVLCILTYGMMSSNVYYYTRMMSQLFLDTPVSKTEKTNFKTLSSMEDFWKFTEGSLLDGLYWKMQPSNQTEADNRSFIFYENLLLGVPRIRQLRVRNGSCSIPQDLRDEIKECYDVYSVSSEDRAPFGPRNGTAWIYTSEKDLNGSSHWGIIATYSGAGYYLDLSRTREETAAQVASLKKNVWLDRGTRATFIDFSVYNANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLI ->DASH_5K47_A||247||526 -NANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLIRKGYH ->DASH_5K47_A||2||537 -PRVAWAERLVRGLRGLWGTRLMEESSTNREKYLKSVLRELVTYLLFLIVLCILTYGMMSSNVYYYTRMMSQLFLDTPVSKTEKTNFKTLSSMEDFWKFTEGSLLDGLYWKMQPSNQTEADNRSFIFYENLLLGVPRIRQLRVRNGSCSIPQDLRDEIKECYDVYSVSSEDRAPFGPRNGTAWIYTSEKDLNGSSHWGIIATYSGAGYYLDLSRTREETAAQVASLKKNVWLDRGTRATFIDFSVYNANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLIRKGYHKALVKLKLKKN ->DASH_5K47_A||30||525 -REKYLKSVLRELVTYLLFLIVLCILTYGMMSSNVYYYTRMMSQLFLDTPVSKTEKTNFKTLSSMEDFWKFTEGSLLDGLYWKMQPSNQTEADNRSFIFYENLLLGVPRIRQLRVRNGSCSIPQDLRDEIKECYDVYSVSSEDRAPFGPRNGTAWIYTSEKDLNGSSHWGIIATYSGAGYYLDLSRTREETAAQVASLKKNVWLDRGTRATFIDFSVYNANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLIRKGY ->DASH_5MKF_A||158||704 -EDQGPPCPSPVGGGDPLHRHLPLEGQPPRVAWAERLVRGLRGLWGTRLMEESSTNREKYLKSVLRELVTYLLFLIVLCILTYGMMSSNVYYYTRMMSQLFLDTPVSKTEKTNFKTLSSMEDFWKFTEGSLLDGLYWKMQPSNQTEADNRSFIFYENLLLGVPRIRQLRVRNGSCSIPQDLRDEIKECYDVYSVSSEDRAPFGPRNGTAWIYTSEKDLNGSSHWGIIATYSGAGYYLDLSRTREETAAQVASLKKNVWLDRGTRATFIDFSVYNANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLI ->DASH_5MKF_A||185||720 -PRVAWAERLVRGLRGLWGTRLMEESSTNREKYLKSVLRELVTYLLFLIVLCILTYGMMSSNVYYYTRMMSQLFLDTPVSKTEKTNFKTLSSMEDFWKFTEGSLLDGLYWKMQPSNQTEADNRSFIFYENLLLGVPRIRQLRVRNGSCSIPQDLRDEIKECYDVYSVSSEDRAPFGPRNGTAWIYTSEKDLNGSSHWGIIATYSGAGYYLDLSRTREETAAQVASLKKNVWLDRGTRATFIDFSVYNANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLIRKGYHKALVKLKLKKN ->DASH_5MKF_A||430||709 -NANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLIRKGYH ->DASH_5TJA_A||3||217 -GLSNQLAVTFREENTIAFRHLFLLGYSDGADDTFAAYTREQLYQAIFHAVDQYLALPDVSLGRYAYVRGGGDPWTNGSGLALCQRYYHRGHVDPANDTFDIDPMVVTDCIQVDPPERPPPPPSDDLTLLESSSSYKNLTLKFHKLVNVTIHFRLKTINLQSLINNEIPDCYTFSVLITFDNKAHSGRIPISLETQAHIQECKHPSVFQHGDNSLE ->DASH_5VKQ_A||1228||1596 -DKRNVEFLDVLIENEQKEVIAHTVVQRYLQELWHGSLTWASWKILLLLVAFIVCPPVWIGFTFPMGHKFNKVPIIKFMSYLTSHIYLMIHLSIVGITPIYPVLRLSLVPYWYEVGLLIWLSGLLLFELTNPSDKSGLGSIKVLVLLLGMAGVGVHVSAFLFVSKEYWPTLVYCRNQCFALAFLLACVQILDFLSFHHLFGPWAIIIGDLLKDLARFLAVLAIFVFGFSMHIVALNQSFANFSPEDLRSFEKKNRNRGYFSDVRMHPINSFELLFFAVFGQTTTEQTQVDKIKNVATPTQPYWVEYLFKIVFGIYMLVSVVVLIQLLIAMMSDTYQRIQAQSDIEWKFGLSKLIRNMHRTTTAPSPLNLV ->DASH_5W3S_A||14||541 -HEEENRCNFNQHTSPSEELLLEDQMRRKLKFFFMNPCEKFWARGRKPWKLAIQILKIAMVTIQLVLFGLSNQMVVAFKEENTVAFKHLFLKGYIDRMDDTYAVYTQSDVYDQIIFAVNQYLQLYQVSVGNHAYENKGTDQSAMAICQHFYKRGNIYPGNDTFDIDPEIETDCFFVEPDEPFHIGTPAENKLNLTLDFHRLLTVELQFKLKAINLQTVRHQELPDCYDFTLTITFDNKAHSGRIKISLDNDISIRECKDWHVSGSIQKNTHNMMIFDAFVILTCLVSLILCIRSVISGLQLQQEFVNFFLLHYKKDVSVSDQMEFVNGWYIMIIISDILTIIGSILKMEIQAKSLTSYDVCSILLGTSTMLVWLGVIRYLGFFAKYNLLILTLQAALPNVIRFCCCAAMIYLGYCFCGWIVLGPYHNKFRSLNMVSECLFSLINGDDMFATFAKMQQKSYLVWLFSRIYLYSFISLFIYMILSLFIALITDTYETIKHYQQDGFPETELRTFISECKDLPNSGKFRLED ->DASH_5W3S_A||28||546 -PSEELLLEDQMRRKLKFFFMNPCEKFWARGRKPWKLAIQILKIAMVTIQLVLFGLSNQMVVAFKEENTVAFKHLFLKGYIDRMDDTYAVYTQSDVYDQIIFAVNQYLQLYQVSVGNHAYENKGTDQSAMAICQHFYKRGNIYPGNDTFDIDPEIETDCFFVEPDEPFHIGTPAENKLNLTLDFHRLLTVELQFKLKAINLQTVRHQELPDCYDFTLTITFDNKAHSGRIKISLDNDISIRECKDWHVSGSIQKNTHNMMIFDAFVILTCLVSLILCIRSVISGLQLQQEFVNFFLLHYKKDVSVSDQMEFVNGWYIMIIISDILTIIGSILKMEIQAKSLTSYDVCSILLGTSTMLVWLGVIRYLGFFAKYNLLILTLQAALPNVIRFCCCAAMIYLGYCFCGWIVLGPYHNKFRSLNMVSECLFSLINGDDMFATFAKMQQKSYLVWLFSRIYLYSFISLFIYMILSLFIALITDTYETIKHYQQDGFPETELRTFISECKDLPNSGKFRLEDDPPVS ->DASH_5WJ9_A||16||557 -LTPNPGYGTQAGPSPAPPTPPEEEDLRRRLKYFFMSPCDKFRAKGRKPCKLMLQVVKILVVTVQLILFGLSNQLAVTFREENTIAFRHLFLLGYSDGADDTFAAYTREQLYQAIFHAVDQYLALPDVSLGRYAYVRGGGDPWTNGSGLALCQRYYHRGHVDPANDTFDIDPMVVTDCIQVDPPERPPPPPSDDLTLLESSSSYKNLTLKFHKLVNVTIHFRLKTINLQSLINNEIPDCYTFSVLITFDNKAHSGRIPISLETQAHIQECKHPSVFQHGDNSFRLLFDVVVILTCSLSFLLCARSLLRGFLLQNEFVGFMWRQRGRVISLWERLEFVNGWYILLVTSDVLTISGTIMKIGIEAKNLASYDVCSILLGTSTLLVWVGVIRYLTFFHNYNILIATLRVALPSVMRFCCCVAVIYLGYCFCGWIVLGPYHVKFRSLSMVSECLFSLINGDDMFVTFAAMQAQQGRSSLVWLFSQLYLYSFISLFIYMVLSLFIALITGAYDTIKHPGGAGAEESELQAYIAQCQDSPTSGKFRRGS ->DASH_5WPV_A||16||557 -LTPNPGYGTQVGTSPAPTTPTEEEDLRRRLKYFFMSPCDKFRAKGRKPCKLMLQVVKILVVTVQLILFGLSNQLVVTFREENTIAFRHLFLLGYSDGSDDTFAAYTQEQLYQAIFYAVDQYLILPEISLGRYAYVRGGGGPWANGSALALCQRYYHRGHVDPANDTFDIDPRVVTDCIQVDPPDRPPDIPSEDLDFLDGSASYKNLTLKFHKLINVTIHFQLKTINLQSLINNEIPDCYTFSILITFDNKAHSGRIPIRLETKTHIQECKHPSVSRHGDNSFRLLFDVVVILTCSLSFLLCARSLLRGFLLQNEFVVFMWRRRGREISLWERLEFVNGWYILLVTSDVLTISGTVMKIGIEAKNLASYDVCSILLGTSTLLVWVGVIRYLTFFHKYNILIATLRVALPSVMRFCCCVAVIYLGYCFCGWIVLGPYHVKFRSLSMVSECLFSLINGDDMFVTFAAMQAQQGHSSLVWLFSQLYLYSFISLFIYMVLSLFIALITGAYDTIKHPGGTGTEKSELQAYIEQCQDSPTSGKFRRGS ->DASH_5Z1W_A||127||515 -YENLLLGAPRLRQLRVRNDSCVVHEDFREDILNCYDVYSPDKEDQLPFGPQNGTAWTYHSQNELGGSSHWGRLTSYSGGGYYLDLPGSRQASAEALQGLQEGLWLDRGTRVVFIDFSVYNANINLFCILRLVVEFPATGGTIPSWQIRTVKLIRYVNNWDFFIVGCEVVFCVFIFYYVVEEILEIHLHRLRYLSSVWNILDLVVILLSIVAVGFHIFRTLEVNRLMGKLLQQPDTYADFEFLAFWQTQYNNMNAVNLFFAWIKIFKYISFNKTMTQLSSTLARCAKDILGFAIMFFIVFFAYAQLGYLLFGTQVENFSTFVKCIFTQFRIILGDFDYNAIDNANRILGPVYFVTYVFFVFFVLLNMFLAIINDTYSEVKEELAGQKDQL ->DASH_5Z1W_A||13||506 -SIRGLWGTTLTENTAENRELYVKTTLRELVVYIVFLVDICLLTYGMTSSSAYYYTKVMSELFLHTPSDSGVSFQTISSMSDFWDFAQGPLLDSLYWTKWYNNQSLGRGSHSFIYYENLLLGAPRLRQLRVRNDSCVVHEDFREDILNCYDVYSPDKEDQLPFGPQNGTAWTYHSQNELGGSSHWGRLTSYSGGGYYLDLPGSRQASAEALQGLQEGLWLDRGTRVVFIDFSVYNANINLFCILRLVVEFPATGGTIPSWQIRTVKLIRYVNNWDFFIVGCEVVFCVFIFYYVVEEILEIHLHRLRYLSSVWNILDLVVILLSIVAVGFHIFRTLEVNRLMGKLLQQPDTYADFEFLAFWQTQYNNMNAVNLFFAWIKIFKYISFNKTMTQLSSTLARCAKDILGFAIMFFIVFFAYAQLGYLLFGTQVENFSTFVKCIFTQFRIILGDFDYNAIDNANRILGPVYFVTYVFFVFFVLLNMFLAIINDTYSEVKE ->DASH_5Z1W_A||246||537 -NANINLFCILRLVVEFPATGGTIPSWQIRTVKLIRYVNNWDFFIVGCEVVFCVFIFYYVVEEILEIHLHRLRYLSSVWNILDLVVILLSIVAVGFHIFRTLEVNRLMGKLLQQPDTYADFEFLAFWQTQYNNMNAVNLFFAWIKIFKYISFNKTMTQLSSTLARCAKDILGFAIMFFIVFFAYAQLGYLLFGTQVENFSTFVKCIFTQFRIILGDFDYNAIDNANRILGPVYFVTYVFFVFFVLLNMFLAIINDTYSEVKEELAGQKDQLQLSDFLKQSYNKTLLRLRLRKE ->DASH_5Z1W_A||29||447 -NRELYVKTTLRELVVYIVFLVDICLLTYGMTSSSAYYYTKVMSELFLHTPSDSGVSFQTISSMSDFWDFAQGPLLDSLYWTKWYNNQSLGRGSHSFIYYENLLLGAPRLRQLRVRNDSCVVHEDFREDILNCYDVYSPDKEDQLPFGPQNGTAWTYHSQNELGGSSHWGRLTSYSGGGYYLDLPGSRQASAEALQGLQEGLWLDRGTRVVFIDFSVYNANINLFCILRLVVEFPATGGTIPSWQIRTVKLIRYVNNWDFFIVGCEVVFCVFIFYYVVEEILEIHLHRLRYLSSVWNILDLVVILLSIVAVGFHIFRTLEVNRLMGKLLQQPDTYADFEFLAFWQTQYNNMNAVNLFFAWIKIFKYISFNKTMTQLSSTLARCAKDILGFAIMFFIVFFAYAQLGYLLFGTQVENFSTFV ->DASH_5Z1W_A||41||508 -LVVYIVFLVDICLLTYGMTSSSAYYYTKVMSELFLHTPSDSGVSFQTISSMSDFWDFAQGPLLDSLYWTKWYNNQSLGRGSHSFIYYENLLLGAPRLRQLRVRNDSCVVHEDFREDILNCYDVYSPDKEDQLPFGPQNGTAWTYHSQNELGGSSHWGRLTSYSGGGYYLDLPGSRQASAEALQGLQEGLWLDRGTRVVFIDFSVYNANINLFCILRLVVEFPATGGTIPSWQIRTVKLIRYVNNWDFFIVGCEVVFCVFIFYYVVEEILEIHLHRLRYLSSVWNILDLVVILLSIVAVGFHIFRTLEVNRLMGKLLQQPDTYADFEFLAFWQTQYNNMNAVNLFFAWIKIFKYISFNKTMTQLSSTLARCAKDILGFAIMFFIVFFAYAQLGYLLFGTQVENFSTFVKCIFTQFRIILGDFDYNAIDNANRILGPVYFVTYVFFVFFVLLNMFLAIINDTYSEVKEEL ->DASH_5Z1W_A||9||528 -HICRSIRGLWGTTLTENTAENRELYVKTTLRELVVYIVFLVDICLLTYGMTSSSAYYYTKVMSELFLHTPSDSGVSFQTISSMSDFWDFAQGPLLDSLYWTKWYNNQSLGRGSHSFIYYENLLLGAPRLRQLRVRNDSCVVHEDFREDILNCYDVYSPDKEDQLPFGPQNGTAWTYHSQNELGGSSHWGRLTSYSGGGYYLDLPGSRQASAEALQGLQEGLWLDRGTRVVFIDFSVYNANINLFCILRLVVEFPATGGTIPSWQIRTVKLIRYVNNWDFFIVGCEVVFCVFIFYYVVEEILEIHLHRLRYLSSVWNILDLVVILLSIVAVGFHIFRTLEVNRLMGKLLQQPDTYADFEFLAFWQTQYNNMNAVNLFFAWIKIFKYISFNKTMTQLSSTLARCAKDILGFAIMFFIVFFAYAQLGYLLFGTQVENFSTFVKCIFTQFRIILGDFDYNAIDNANRILGPVYFVTYVFFVFFVLLNMFLAIINDTYSEVKEELAGQKDQLQLSDFLKQSYNKT ->DASH_5Z96_A||286||659 -LARLKLAIKYRQKEFVAQPNCQQLLASRWYDEFPGWRRRHWAVKMVTCFIIGLLFPVFSVCYLIAPKSPLGLFIRKPFIKFICHTASYLTFLFLLLLASQHIDRSDLNRQGPPPTIVEWMILPWVLGFIWGEIKQMWDGGLQDYIHDWWNLMDFVMNSLYLATISLKIVAFVKYSALNPRESWDMWHPTLVAEALFAIANIFSSLRLISLFTANSHLGPLQISLGRMLLDILKFLFIYCLVLLAFANGLNQLYFYYEETKGLSCKGIRCEKQNNAFSTLFETLQSLFWSIFGLINLYVTNVKAQHEFTEFVGATMFGTYNVISLVVLLNMLIAMMNNSYQLIADHADIEWKFARTKLWMSYFEEGGTLPTPFNV ->DASH_5Z96_A||289||660 -LKLAIKYRQKEFVAQPNCQQLLASRWYDEFPGWRRRHWAVKMVTCFIIGLLFPVFSVCYLIAPKSPLGLFIRKPFIKFICHTASYLTFLFLLLLASQHIDRSDLNRQGPPPTIVEWMILPWVLGFIWGEIKQMWDGGLQDYIHDWWNLMDFVMNSLYLATISLKIVAFVKYSALNPRESWDMWHPTLVAEALFAIANIFSSLRLISLFTANSHLGPLQISLGRMLLDILKFLFIYCLVLLAFANGLNQLYFYYEETKGLSCKGIRCEKQNNAFSTLFETLQSLFWSIFGLINLYVTNVKAQHEFTEFVGATMFGTYNVISLVVLLNMLIAMMNNSYQLIADHADIEWKFARTKLWMSYFEEGGTLPTPFNVI ->DASH_5Z96_A||290||663 -KLAIKYRQKEFVAQPNCQQLLASRWYDEFPGWRRRHWAVKMVTCFIIGLLFPVFSVCYLIAPKSPLGLFIRKPFIKFICHTASYLTFLFLLLLASQHIDRSDLNRQGPPPTIVEWMILPWVLGFIWGEIKQMWDGGLQDYIHDWWNLMDFVMNSLYLATISLKIVAFVKYSALNPRESWDMWHPTLVAEALFAIANIFSSLRLISLFTANSHLGPLQISLGRMLLDILKFLFIYCLVLLAFANGLNQLYFYYEETKGLSCKGIRCEKQNNAFSTLFETLQSLFWSIFGLINLYVTNVKAQHEFTEFVGATMFGTYNVISLVVLLNMLIAMMNNSYQLIADHADIEWKFARTKLWMSYFEEGGTLPTPFNVIPSP ->DASH_5ZX5_A||814||1056 -FKEVKILDSSDGKNEMEIHIKSKKLPITRKFYAFYHAPIVKFWFNTLAYLGFLMLYTFVVLVKMEQLPSVQEWIVIAYIFTYAIEKVREVFMSEAGKISQKIKVWFSDYFNVSDTIAIISFFVGFGLRFGAKWNYINAYDNHVFVAGRLIYCLNIIFWYVRLLDFLAVNQQAGPYVMMIGKMVANMFYIVVIMALVLLSFGVPRKAILYPHEEPSWSLAKDIVFHPYWMIFGEVYAYEIDVCA ->DASH_5ZX5_A||820||1131 -LDSSDGKNEMEIHIKSKKLPITRKFYAFYHAPIVKFWFNTLAYLGFLMLYTFVVLVKMEQLPSVQEWIVIAYIFTYAIEKVREVFMSEAGKISQKIKVWFSDYFNVSDTIAIISFFVGFGLRFGAKWNYINAYDNHVFVAGRLIYCLNIIFWYVRLLDFLAVNQQAGPYVMMIGKMVANMFYIVVIMALVLLSFGVPRKAILYPHEEPSWSLAKDIVFHPYWMIFGEVYAYEIDVCANDSTLPTICGPGTWLTPFLQAVYLFVQYIIMVNLLIAFFNNVYLQVKAISNIVWKYQRYHFIMAYHEKPVLPPPL ->DASH_5ZX5_A||821||1134 -DSSDGKNEMEIHIKSKKLPITRKFYAFYHAPIVKFWFNTLAYLGFLMLYTFVVLVKMEQLPSVQEWIVIAYIFTYAIEKVREVFMSEAGKISQKIKVWFSDYFNVSDTIAIISFFVGFGLRFGAKWNYINAYDNHVFVAGRLIYCLNIIFWYVRLLDFLAVNQQAGPYVMMIGKMVANMFYIVVIMALVLLSFGVPRKAILYPHEEPSWSLAKDIVFHPYWMIFGEVYAYEIDVCANDSTLPTICGPGTWLTPFLQAVYLFVQYIIMVNLLIAFFNNVYLQVKAISNIVWKYQRYHFIMAYHEKPVLPPPLIIL ->DASH_5ZX5_A||827||1228 -NEMEIHIKSKKLPITRKFYAFYHAPIVKFWFNTLAYLGFLMLYTFVVLVKMEQLPSVQEWIVIAYIFTYAIEKVREVFMSEAGKISQKIKVWFSDYFNVSDTIAIISFFVGFGLRFGAKWNYINAYDNHVFVAGRLIYCLNIIFWYVRLLDFLAVNQQAGPYVMMIGKMVANMFYIVVIMALVLLSFGVPRKAILYPHEEPSWSLAKDIVFHPYWMIFGEVYAYEIDVCANDSTLPTICGPGTWLTPFLQAVYLFVQYIIMVNLLIAFFNNVYLQVKAISNIVWKYQRYHFIMAYHEKPVLPPPLIILSHIVSLFCCVCKRRKKDKTSDGPKLFLTEEDQKKLHDFEEQCVEMYFDEKDDKFNSGSEERIRVTFERVEQMSIQIKEVGDRVNYIKRSLQSLD ->DASH_6A70_A||27||559 -SHPQFEKGSAAAPRVAWAERLVRGLRGLWGTRLMEESSTNREKYLKSVLRELVTYLLFLIVLCILTYGMMSSNVYYYTRMMSQLFLDTPVSKTEKTNFKTLSSMEDFWKFTEGSLLDGLYWKMQPSNQTEADNRSFIFYENLLLGVPRIRQLRVRNGSCSIPQDLRDEIKECYDVYSVSSEDRAPFGPRNGTAWIYTSEKDLNGSSHWGIIATYSGAGYYLDLSRTREETAAQVASLKKNVWLDRGTRATFIDFSVYNANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLIR ->DASH_6A70_A||284||563 -NANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLIRKGYH ->DASH_6A70_A||39||574 -PRVAWAERLVRGLRGLWGTRLMEESSTNREKYLKSVLRELVTYLLFLIVLCILTYGMMSSNVYYYTRMMSQLFLDTPVSKTEKTNFKTLSSMEDFWKFTEGSLLDGLYWKMQPSNQTEADNRSFIFYENLLLGVPRIRQLRVRNGSCSIPQDLRDEIKECYDVYSVSSEDRAPFGPRNGTAWIYTSEKDLNGSSHWGIIATYSGAGYYLDLSRTREETAAQVASLKKNVWLDRGTRATFIDFSVYNANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLIRKGYHKALVKLKLKKN ->DASH_6A70_A||67||562 -REKYLKSVLRELVTYLLFLIVLCILTYGMMSSNVYYYTRMMSQLFLDTPVSKTEKTNFKTLSSMEDFWKFTEGSLLDGLYWKMQPSNQTEADNRSFIFYENLLLGVPRIRQLRVRNGSCSIPQDLRDEIKECYDVYSVSSEDRAPFGPRNGTAWIYTSEKDLNGSSHWGIIATYSGAGYYLDLSRTREETAAQVASLKKNVWLDRGTRATFIDFSVYNANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLIRKGY ->DASH_6A70_B||227||1129 -LRFRRLLVAELQRGFFDKHIWLSIWDRPPRSRFTRIQRATCCVLLICLFLGANAVWYGAVGDSAYSTGHVSRLSPLSVDTVAVGLVSSVVVYPVYLAILFLFRMSRSKVAGSPSPTPAGQQVLDIDSCLDSSVLDSSFLTFSGLHAEQAFVGQMKSDLFLDDSKSLVCWPSGEGTLSWPDLLSDPSIVGSNLRQLARGQAGHGLGPEEDGFSLASPYSPAKSFSASDEDLIQQVLAEGVSSPAPTQDTHMETDLLSSLSSTPGEKTETLALQRLGELGPPSPGLNWEQPQAARLSRTGLVEGLRKRLLPAWCASLAHGLSLLLVAVAVAVSGWVGASFPPGVSVAWLLSSSASFLASFLGWEPLKVLLEALYFSLVAKRLHPDEDDTLVESPAVTPVSARVPRVRPPHGFALFLAKEEARKVKRLHGMLRSLLVYMLFLLVTLLASYGDASCHGHAYRLQSAIKQELHSRAFLAITRSEELWPWMAHVLLPYVHGNQSSPELGPPRLRQVRLQEALYPDPPGPRVHTCSAAGGFSTSDYDVGWESPHNGSGTWAYSAPDLLGAWSWGSCAVYDSGGYVQELGLSLEESRDRLRFLQLHNWLDNRSRAVFLELTRYSPAVGLHAAVTLRLEFPAAGRALAALSVRPFALRRLSAGLSLPLLTSVCLLLFAVHFAVAEARTWHREGRWRVLRLGAWARWLLVALTAATALVRLAQLGAADRQWTRFVRGRPRRFTSFDQVAQLSSAARGLAASLLFLLLVKAAQQLRFVRQWSVFGKTLCRALPELLGVTLGLVVLGVAYAQLAILLVSSCVDSLWSVAQALLVLCPGTGLSTLCPAESWHLSPLLCVGLWALRLWGALRLGAVILRWRYHALRGELYRPAWEPQDYEMVELFLRRLRLWMGLSK ->DASH_6AEI_A||287||663 -LAKLKVAIKYHQKEFVAQPNCQQLLATLWYDGFPGWRRKHWVVKLLTCMTIGFLFPMLSIAYLISPRSNLGLFIKKPFIKFICHTASYLTFLFMLLLASQHIVRTDLHVQGPPPTVVEWMILPWVLGFIWGEIKEMWDGGFTEYIHDWWNLMDFAMNSLYLATISLKIVAYVKYNGSRPREEWEMWHPTLIAEALFAISNILSSLRLISLFTANSHLGPLQISLGRMLLDILKFLFIYCLVLLAFANGLNQLYFYYETRAIDEPNNCKGIRCEKQNNAFSTLFETLQSLFWSVFGLLNLYVTNVKARHEFTEFVGATMFGTYNVISLVVLLNMLIAMMNNSYQLIADHADIEWKFARTKLWMSYFDEGGTLPPPFNI ->DASH_6AEI_A||290||664 -LKVAIKYHQKEFVAQPNCQQLLATLWYDGFPGWRRKHWVVKLLTCMTIGFLFPMLSIAYLISPRSNLGLFIKKPFIKFICHTASYLTFLFMLLLASQHIVRTDLHVQGPPPTVVEWMILPWVLGFIWGEIKEMWDGGFTEYIHDWWNLMDFAMNSLYLATISLKIVAYVKYNGSRPREEWEMWHPTLIAEALFAISNILSSLRLISLFTANSHLGPLQISLGRMLLDILKFLFIYCLVLLAFANGLNQLYFYYETRAIDEPNNCKGIRCEKQNNAFSTLFETLQSLFWSVFGLLNLYVTNVKARHEFTEFVGATMFGTYNVISLVVLLNMLIAMMNNSYQLIADHADIEWKFARTKLWMSYFDEGGTLPPPFNII ->DASH_6AEI_A||291||667 -KVAIKYHQKEFVAQPNCQQLLATLWYDGFPGWRRKHWVVKLLTCMTIGFLFPMLSIAYLISPRSNLGLFIKKPFIKFICHTASYLTFLFMLLLASQHIVRTDLHVQGPPPTVVEWMILPWVLGFIWGEIKEMWDGGFTEYIHDWWNLMDFAMNSLYLATISLKIVAYVKYNGSRPREEWEMWHPTLIAEALFAISNILSSLRLISLFTANSHLGPLQISLGRMLLDILKFLFIYCLVLLAFANGLNQLYFYYETRAIDEPNNCKGIRCEKQNNAFSTLFETLQSLFWSVFGLLNLYVTNVKARHEFTEFVGATMFGTYNVISLVVLLNMLIAMMNNSYQLIADHADIEWKFARTKLWMSYFDEGGTLPPPFNIIPSP ->DASH_6AYF_A||19||546 -HEEENRCNFNQQTSPSEELLLEDQMRRKLKFFFMNPCEKFWARGRKPWKLAIQILKIAMVTIQLVLFGLSNQMVVAFKEENTIAFKHLFLKGYMDRMDDTYAVYTQSDVYDQLIFAVNQYLQLYNVSVGNHAYENKGTKQSAMAICQHFYKRGNIYPGNDTFDIDPEIETECFFVEPDEPFHIGTPAENKLNLTLDFHRLLTVELQFKLKAINLQTVRHQELPDCYDFTLTITFDNKAHSGRIKISLDNDISIRECKDWHVSGSIQKNTHYMMIFDAFVILTCLVSLILCIRSVIRGLQLQQEFVNFFLLHYKKEVSVSDQMEFVNGWYIMIIISDILTIIGSILKMEIQAKSLTSYDVCSILLGTSTMLVWLGVIRYLGFFAKYNLLILTLQAALPNVIRFCCCAAMIYLGYCFCGWIVLGPYHDKFRSLNMVSECLFSLINGDDMFATFAKMQQKSYLVWLFSRIYLYSFISLFIYMILSLFIALITDTYETIKQYQQDGFPETELRTFISECKDLPNSGKYRLED ->DASH_6BBJ_A||424||746 -GEEVSVLEILVYNSKVENRHEMLAVEPINELLRDKWQKFGAVSFYISVVSYLIAMIIFTLIAYYRPMDGTPPYPYRTTMDYMRLAGEIVTLLTGVVFFITNIKDLFMKKCPGVNSLFIDGSFQLLYFIYSVLVIITAVLYLVGIESYLAVMVFALVLGWMNALYFTRGLKLTGTYSIMLQKILFKDLFRFLLVYLLFMIGYASALVSLLNPCTSQESCIETSSNCTVPEYPSCRDSSTFSKFLLDLFKLTIGMGDLEMINSAKYPAVFIILLVTYIILTFVLLLNMLIALMGETVGQVSKESKQIWKLQWATTILDIERSFPV ->DASH_6BBJ_A||428||750 -SVLEILVYNSKVENRHEMLAVEPINELLRDKWQKFGAVSFYISVVSYLIAMIIFTLIAYYRPMDGTPPYPYRTTMDYMRLAGEIVTLLTGVVFFITNIKDLFMKKCPGVNSLFIDGSFQLLYFIYSVLVIITAVLYLVGIESYLAVMVFALVLGWMNALYFTRGLKLTGTYSIMLQKILFKDLFRFLLVYLLFMIGYASALVSLLNPCTSQESCIETSSNCTVPEYPSCRDSSTFSKFLLDLFKLTIGMGDLEMINSAKYPAVFIILLVTYIILTFVLLLNMLIALMGETVGQVSKESKQIWKLQWATTILDIERSFPVCMRK ->DASH_6BCO_A||735||1081 -PPGTVEPSAKVALERRQRRRPGRALCCGKFSKRWSDFWGAPVTAFLGNVVSYLLFLLLFAHVLLVDFQPTKPSVSELLLYFWAFTLLCEELRQGLGGGWGSLASGGRGPDRAPLRHRLHLYLSDTWNQCDLLALTCFLLGVGCRLTPGLFDLGRTVLCLDFMIFTLRLLHIFTVNKQLGPKIVIVSKMMKDVFFFLFFLCVWLVAYGVATEGILRPQDRSLPSILRRVFYRPYLQIFGQIPQEEMDVALMIPGNCSMERGSWAHPEGPVAGSCVSQYANWLVVLLLIVFLLVANILLLNLLIAMFSYTFSKVHGNSDLYWKAQRYSLIREFHSRPALAPPLIIISHV ->DASH_6BO5_A||314||642 -NSVLEIIAFHCKSPNRHRMVVLEPLNKLLQEKWDRLVSRFFFNFACYLVYMFIFTVVAYHQPSLDQPAIPSSKATFGESMLLLGHILILLGGIYLLLGQLWYFWRRRLFIWISFMDSYFEILFLLQALLTVLSQVLRFMETEWYLPLLVLSLVLGWLNLLYYTRGFQHTGIYSVMIQKVILRDLLRFLLVYLVFLFGFAVALVSLSREARSPKAPEDNNSTVTEQPTVGQEEEPAPYRSILDASLELFKFTIGMGELAFQEQLRFRGVVLLLLLAYVLLTYVLLLNMLIALMSETVNHVADNSWSIWKLQKAISVLEMENGYWWCRRKK ->DASH_6BO8_A||288||614 -DEQSLLELIITTKKREARQILDQTPVKELVSLKWKRYGRPYFCMLGAIYLLYIICFTMCCIYRPLKPRTNNRTSPRDNTLLQQKLLQEAYMTPKDDIRLVGELVTVIGAIIILLVEVPDIFRMGVTRFFGQTILGGPFHVLIITYAFMVLVTMVMRLISASGEVVPMSFALVLGWCNVMYFARGFQMLGPFTIMIQKMIFGDLMRFCWLMAVVILGFASAFYIIFQTEDPEELGHFYDYPMALFSTFELFLTIIDGPANYNVDLPFMYSITYAAFAIIATLLMLNLLIAMMGDTHWRVAHERDELWRAQIVATTVMLERKLPRCLWP ->DASH_6BO8_A||384||609 -IRLVGELVTVIGAIIILLVEVPDIFRMGVTRFFGQTILGGPFHVLIITYAFMVLVTMVMRLISASGEVVPMSFALVLGWCNVMYFARGFQMLGPFTIMIQKMIFGDLMRFCWLMAVVILGFASAFYIIFQTEDPEELGHFYDYPMALFSTFELFLTIIDGPANYNVDLPFMYSITYAAFAIIATLLMLNLLIAMMGDTHWRVAHERDELWRAQIVATTVMLERKLP ->DASH_6BPQ_A||570||883 -IILCLFFFPLIGCGFISFRKKPVEKTKKLFLYYVSFFTSPFVVFSWNVIFYIAFLLLFAYVLLMDFQKEPTALEIILYVLVFILLCDEVRQWYMNGSKYFSDLWNVMDTLAIFYFIAGIVFRLHSDESSWYSGRVIFCLDYIVFTLRLIHIFTVSRNLGPKIIMLQRMMIDVFFFLFLFAVWMVAFGVARQGILRKNEHRWEWIFRSVIYEPYLAMFGQYPDDIDGTTYNFDHCTFSGNESKPLCVELDANNQPRFPEWITIPLVCIYMLSTNILLVNLLVAMFGYTVGSVQENNDQVWKFQRFFLVQEYCSRL ->DASH_6BQR_A||661||1011 -PVGTADPAEKTPLGVPRQSGRPGCCGGRCGGRRCLRRWFHFWGAPVTIFMGNVVSYLLFLLLFSRVLLVDFQPAPPGSLELLLYFWAFTLLCEELRQGLSGGGGSLASGGPGPGHASLSQRLRLYLADSWNQCDLVALTCFLLGVGCRLTPGLYHLGRTVLCIDFMVFTVRLLHIFTVNKQLGPKIVIVSKMMKDVFFFLFFLGVWLVAYGVATEGLLRPRDSDFPSILRRVFYRPYLQIFGQIPQEDMDVALMEHSNCSSEPGFWAHPPGAQAGTCVSQYANWLVVLLLVIFLLVANILLVNLLIAMFSYTFGKVQGNSDLYWKAQRYRLIREFHSRPALAPPFIVISHL ->DASH_6BQV_A||739||1089 -PVGTADPAEKTPLGVPRQSGRPGCCGGRCGGRRCLRRWFHFWGAPVTIFMGNVVSYLLFLLLFSRVLLVDFQPAPPGSLELLLYFWAFTLLCEELRQGLSGGGGSLASGGPGPGHASLSQRLRLYLADSWNQCDLVALTCFLLGVGCRLTPGLYHLGRTVLCIDFMVFTVRLLHIFTVNKQLGPKIVIVSKMMKDVFFFLFFLGVWLVAYGVATEGLLRPRDSDFPSILRRVFYRPYLQIFGQIPQEDMDVALMEHSNCSSEPGFWAHPPGAQAGTCVSQYANWLVVLLLVIFLLVANILLVNLLIAMFSYTFGKVQGNSDLYWKAQRYRLIREFHSRPALAPPFIVISHL ->DASH_6BWD_A||470||712 -FKEVKILDSSDGKNEMEIHIKSKKLPITRKFYAFYHAPIVKFWFNTLAYLGFLMLYTFVVLVKMEQLPSVQEWIVIAYIFTYAIEKVREVFMSEAGKISQKIKVWFSDYFNVSDTIAIISFFVGFGLRFGAKWNYINAYDNHVFVAGRLIYCLNIIFWYVRLLDFLAVNQQAGPYVMMIGKMVANMFYIVVIMALVLLSFGVPRKAILYPHEEPSWSLAKDIVFHPYWMIFGEVYAYEIDVCA ->DASH_6BWD_A||476||787 -LDSSDGKNEMEIHIKSKKLPITRKFYAFYHAPIVKFWFNTLAYLGFLMLYTFVVLVKMEQLPSVQEWIVIAYIFTYAIEKVREVFMSEAGKISQKIKVWFSDYFNVSDTIAIISFFVGFGLRFGAKWNYINAYDNHVFVAGRLIYCLNIIFWYVRLLDFLAVNQQAGPYVMMIGKMVANMFYIVVIMALVLLSFGVPRKAILYPHEEPSWSLAKDIVFHPYWMIFGEVYAYEIDVCANDSTLPTICGPGTWLTPFLQAVYLFVQYIIMVNLLIAFFNNVYLQVKAISNIVWKYQRYHFIMAYHEKPVLPPPL ->DASH_6BWD_A||477||790 -DSSDGKNEMEIHIKSKKLPITRKFYAFYHAPIVKFWFNTLAYLGFLMLYTFVVLVKMEQLPSVQEWIVIAYIFTYAIEKVREVFMSEAGKISQKIKVWFSDYFNVSDTIAIISFFVGFGLRFGAKWNYINAYDNHVFVAGRLIYCLNIIFWYVRLLDFLAVNQQAGPYVMMIGKMVANMFYIVVIMALVLLSFGVPRKAILYPHEEPSWSLAKDIVFHPYWMIFGEVYAYEIDVCANDSTLPTICGPGTWLTPFLQAVYLFVQYIIMVNLLIAFFNNVYLQVKAISNIVWKYQRYHFIMAYHEKPVLPPPLIIL ->DASH_6BWD_A||480||793 -DGKNEMEIHIKSKKLPITRKFYAFYHAPIVKFWFNTLAYLGFLMLYTFVVLVKMEQLPSVQEWIVIAYIFTYAIEKVREVFMSEAGKISQKIKVWFSDYFNVSDTIAIISFFVGFGLRFGAKWNYINAYDNHVFVAGRLIYCLNIIFWYVRLLDFLAVNQQAGPYVMMIGKMVANMFYIVVIMALVLLSFGVPRKAILYPHEEPSWSLAKDIVFHPYWMIFGEVYAYEIDVCANDSTLPTICGPGTWLTPFLQAVYLFVQYIIMVNLLIAFFNNVYLQVKAISNIVWKYQRYHFIMAYHEKPVLPPPLIILSHI ->DASH_6BWD_A||483||904 -NEMEIHIKSKKLPITRKFYAFYHAPIVKFWFNTLAYLGFLMLYTFVVLVKMEQLPSVQEWIVIAYIFTYAIEKVREVFMSEAGKISQKIKVWFSDYFNVSDTIAIISFFVGFGLRFGAKWNYINAYDNHVFVAGRLIYCLNIIFWYVRLLDFLAVNQQAGPYVMMIGKMVANMFYIVVIMALVLLSFGVPRKAILYPHEEPSWSLAKDIVFHPYWMIFGEVYAYEIDVCANDSTLPTICGPGTWLTPFLQAVYLFVQYIIMVNLLIAFFNNVYLQVKAISNIVWKYQRYHFIMAYHEKPVLPPPLIILSHIVSLFCCVCKRRKKDKTSDGPKLFLTEEDQKKLHDFEEQCVEMYFDEKDDKFNSGSEERIRVTFERVEQMSIQIKEVGDRVNYIKRSLQSLDSQIGHLQDLSALTVDTLKTL ->DASH_6BWI_A||536||886 -PVGTADPAEKTPLGVPRQSGRPGCCGGRCGGRRCLRRWFHFWGAPVTIFMGNVVSYLLFLLLFSRVLLVDFQPAPPGSLELLLYFWAFTLLCEELRQGLSGGGGSLASGGPGPGHASLSQRLRLYLADSWNQCDLVALTCFLLGVGCRLTPGLYHLGRTVLCIDFMVFTVRLLHIFTVNKQLGPKIVIVSKMMKDVFFFLFFLGVWLVAYGVATEGLLRPRDSDFPSILRRVFYRPYLQIFGQIPQEDMDVALMEHSNCSSEPGFWAHPPGAQAGTCVSQYANWLVVLLLVIFLLVANILLVNLLIAMFSYTFGKVQGNSDLYWKAQRYRLIREFHSRPALAPPFIVISHL ->DASH_6BWJ_A||351||680 -NSVLEIIAFHSRSPHRHRMVVLEPLNKLLQAKWDRLIPRFCFNFLCYLVYMLIFTAVAYHQPALEKQGFPPLKATAGNSMLLLGHILILLGGVYLLLGQLWYFWRRRLFIWISFMDSYSEILFLLQALLTVLSQVLCFLAIEWYLPLLVSSLVMGWTNLLYYTRGFQHTGIYSVMIEKVILRDLLRFLLVYLVFLFGFAVALVSLSREAQNSRTPAGPNATEVGQPGAGQEDEAPPYRSILDASLELFKFTIGMGELAFQEQLRFRGVVLLLLLAYVLLTYVLLLNMLIALMSETVNSVATDSWSIWKLQKAISVLEMENGYWWCRRKKQ ->DASH_6C8G_A||293||615 -GEEVSVLEILVYNSKVENRHEMLAVEPINELLRDKWQKFGAVSFYISVVSYLIAMIIFTLIAYYRPMDGTPPYPYRTTMDYMRLAGEIVTLLTGVVFFITNIKDLFMKKCPGVNSLFIDGSFQLLYFIYSVLVIITAVLYLVGIESYLAVMVFALVLGWMNALYFTRGLKLTGTYSIMLQKILFKDLFRFLLVYLLFMIGYASALVSLLNPCTSQESCIETSSQCTVPEYPSCRDSSTFSKFLLDLFKLTIGMGDLEMINSAKYPAVFIILLVTYIILTFVLLLNMLIALMGETVGQVSKESKQIWKLQWATTILDIERSFPV ->DASH_6C8G_A||294||617 -EEVSVLEILVYNSKVENRHEMLAVEPINELLRDKWQKFGAVSFYISVVSYLIAMIIFTLIAYYRPMDGTPPYPYRTTMDYMRLAGEIVTLLTGVVFFITNIKDLFMKKCPGVNSLFIDGSFQLLYFIYSVLVIITAVLYLVGIESYLAVMVFALVLGWMNALYFTRGLKLTGTYSIMLQKILFKDLFRFLLVYLLFMIGYASALVSLLNPCTSQESCIETSSQCTVPEYPSCRDSSTFSKFLLDLFKLTIGMGDLEMINSAKYPAVFIILLVTYIILTFVLLLNMLIALMGETVGQVSKESKQIWKLQWATTILDIERSFPVCM ->DASH_6C8G_A||295||619 -EVSVLEILVYNSKVENRHEMLAVEPINELLRDKWQKFGAVSFYISVVSYLIAMIIFTLIAYYRPMDGTPPYPYRTTMDYMRLAGEIVTLLTGVVFFITNIKDLFMKKCPGVNSLFIDGSFQLLYFIYSVLVIITAVLYLVGIESYLAVMVFALVLGWMNALYFTRGLKLTGTYSIMLQKILFKDLFRFLLVYLLFMIGYASALVSLLNPCTSQESCIETSSQCTVPEYPSCRDSSTFSKFLLDLFKLTIGMGDLEMINSAKYPAVFIILLVTYIILTFVLLLNMLIALMGETVGQVSKESKQIWKLQWATTILDIERSFPVCMRK ->DASH_6C8G_A||419||661 -FIYSVLVIITAVLYLVGIESYLAVMVFALVLGWMNALYFTRGLKLTGTYSIMLQKILFKDLFRFLLVYLLFMIGYASALVSLLNPCTSQESCIETSSQCTVPEYPSCRDSSTFSKFLLDLFKLTIGMGDLEMINSAKYPAVFIILLVTYIILTFVLLLNMLIALMGETVGQVSKESKQIWKLQWATTILDIERSFPVCMRKAFRSGEMVTVGKNLDGTPDRRWCFRVDEVNWSHWNQNLGIIN ->DASH_6CO7_A||808||1043 -EIREDDSMEVIMRNKKLGFCDRIMHFYSAPFSKFVGNVVGYLAFIFLYAYVVLFNFPRFDPAKTLGGIHPTEIVLYFWVFTILIEEIRQLAAKPPKYIKDKVSVYFSDTWNFVDIFSLTVFIIAIILRFFTNSRIFTASRIILSLDIIFFIVRSLQIFSVNRLLGPKLVMIQKMMQDLAQFIIILAVFTIAYGIALHAVMFPSPGIYARNNTWVTITSVVQYPYWQMYGELFLDEI ->DASH_6CO7_A||810||1124 -REDDSMEVIMRNKKLGFCDRIMHFYSAPFSKFVGNVVGYLAFIFLYAYVVLFNFPRFDPAKTLGGIHPTEIVLYFWVFTILIEEIRQLAAKPPKYIKDKVSVYFSDTWNFVDIFSLTVFIIAIILRFFTNSRIFTASRIILSLDIIFFIVRSLQIFSVNRLLGPKLVMIQKMMQDLAQFIIILAVFTIAYGIALHAVMFPSPGIYARNNTWVTITSVVQYPYWQMYGELFLDEIQGEKPKEFGEVDPDGRWLSPLLLAIYMVFTNILLLNLLIAIFNYTFERVQEDSDKVWKFQRYDLVQEYHSRPVFAPPLVLL diff --git a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/disttbfast b/aphylogeo/bin/mafft-linux64/mafftdir/libexec/disttbfast deleted file mode 100755 index 0a876acd..00000000 Binary files a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/disttbfast and /dev/null differ diff --git a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/dndblast b/aphylogeo/bin/mafft-linux64/mafftdir/libexec/dndblast deleted file mode 100755 index 288f6c6d..00000000 Binary files a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/dndblast and /dev/null differ diff --git a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/dndfast7 b/aphylogeo/bin/mafft-linux64/mafftdir/libexec/dndfast7 deleted file mode 100755 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b/aphylogeo/bin/mafft-linux64/mafftdir/libexec/filter deleted file mode 100755 index 863f84b1..00000000 Binary files a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/filter and /dev/null differ diff --git a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/getlag b/aphylogeo/bin/mafft-linux64/mafftdir/libexec/getlag deleted file mode 100755 index 4ab6a90f..00000000 Binary files a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/getlag and /dev/null differ diff --git a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/hat3 b/aphylogeo/bin/mafft-linux64/mafftdir/libexec/hat3 deleted file mode 100644 index e69de29b..00000000 diff --git a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/hex2maffttext b/aphylogeo/bin/mafft-linux64/mafftdir/libexec/hex2maffttext deleted file mode 100755 index a09f48b4..00000000 Binary files a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/hex2maffttext and /dev/null differ diff --git a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/mafft-distance b/aphylogeo/bin/mafft-linux64/mafftdir/libexec/mafft-distance deleted file mode 100755 index 673d655e..00000000 Binary files a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/mafft-distance and /dev/null differ diff --git a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/mafft-homologs.1 b/aphylogeo/bin/mafft-linux64/mafftdir/libexec/mafft-homologs.1 deleted file mode 100755 index a9c96825..00000000 --- a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/mafft-homologs.1 +++ /dev/null @@ -1,131 +0,0 @@ -.\" Title: MAFFT-HOMOLOGS -.\" Author: Kazutaka Katoh -.\" Generator: DocBook XSL Stylesheets v1.72.0 -.\" Date: 2007-08-14 -.\" Manual: Mafft Manual -.\" Source: mafft-homologs 2.1 -.\" -.TH "MAFFT\-HOMOLOGS" "1" "2007\-06\-09" "mafft\-homologs 2.1" "Mafft Manual" -.\" disable hyphenation -.nh -.\" disable justification (adjust text to left margin only) -.ad l -.SH "NAME" -.RS 0 -mafft\-homologs \- aligns sequences together with homologues automatically collected from SwissProt via NCBI BLAST -.RE -.SH "SYNOPSIS" -.RS 0 -\fBmafft\-homologs\fR [\fBoptions\fR] \fIinput\fR [>\ \fIoutput\fR] -.RE -.SH "DESCRIPTION" -.RS 0 -The accuracy of an alignment of a few distantly related sequences is considerably improved when being aligned together with their close homologs. The reason for the improvement is probably the same as that for PSI\-BLAST. That is, the positions of highly conserved residues, those with many gaps and other additional information is brought by close homologs. According to Katoh et al. (2005), the improvement by adding close homologs is 10% or so, which is comparable to the improvement by incorporating structural information of a pair of sequences. Mafft\-homologs in a mafft server works like this: -.sp -.RS 4 -\h'-04' 1.\h'+02'Collect a number (50 by default) of close homologs (E=1e\-10 by default) of the input sequences. -.RE -.sp -.RS 4 -\h'-04' 2.\h'+02'Align the input sequences and homologs all together using the L\-INS\-i strategy. -.RE -.sp -.RS 4 -\h'-04' 3.\h'+02'Remove the homologs. -.RE -.RE -.SH "OPTIONS" -.RS 0 -.PP -\fB\-a\fR \fI\fIn\fR\fR -.RS 4 -The number of collected sequences (default: 50). -.RE -.PP -\fB\-e\fR \fI\fIn\fR\fR -.RS 4 -Threshold value (default: 1e\-10). -.RE -.PP -\fB\-o\fR \fI\fIxxx\fR\fR -.RS 4 -Options for mafft (default: " \-\-op 1.53 \-\-ep 0.123 \-\-maxiterate 1000 --localpair --reorder"). -.RE -.PP -\fB\-l\fR -.RS 4 -Locally carries out BLAST searches instead of NCBI BLAST (requires locally installed BLAST and a database). -.RE -.PP -\fB\-f\fR -.RS 4 -Outputs collected homologues also (default: off). -.RE -.PP -\fB\-w\fR -.RS 4 -entire sequences are subjected to BLAST search (default: well\-aligned region only) -.RE -.RE -.SH "REQUIREMENTS" -.RS 0 -.PP -MAFFT version > 5.58. -.PP -Either of -.RS 4 -.PP -lynx (when remote BLAST server is used) -.PP -BLAST and a protein sequence database (when local BLAST is used) -.RE -.RE -.SH "REFERENCES" -.RS 0 -.PP -Katoh, Kuma, Toh and Miyata (Nucleic Acids Res. 33:511\-518, 2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment. -.RE -.SH "SEE ALSO" -.RS 0 -.PP -\fBmafft\fR(1) -.RE -.SH "AUTHORS" -.RS 0 -.PP -\fBKazutaka Katoh\fR <\&katoh_at_bioreg.kyushu\-u.ac.jp.\&> -.sp -1n -.IP "" 4 -Wrote Mafft. -.PP -\fBCharles Plessy\fR <\&charles\-debian\-nospam@plessy.org\&> -.sp -1n -.IP "" 4 -Wrote this manpage in DocBook XML for the Debian distribution, using Mafft's homepage as a template. -.RE -.SH "COPYRIGHT" -.RS 0 -Copyright \(co 2002\-2007 Kazutaka Katoh (mafft) -.br -Copyright \(co 2007 Charles Plessy (this manpage) -.br -.PP -Mafft and its manpage are offered under the following conditions: -.PP -Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: -.sp -.RS 4 -\h'-04' 1.\h'+02'Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. -.RE -.sp -.RS 4 -\h'-04' 2.\h'+02'Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. -.RE -.sp -.RS 4 -\h'-04' 3.\h'+02'The name of the author may not be used to endorse or promote products derived from this software without specific prior written permission. -.RE -.PP -THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -.br -.RE diff --git a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/mafft-profile b/aphylogeo/bin/mafft-linux64/mafftdir/libexec/mafft-profile deleted file mode 100755 index 91ceedf5..00000000 Binary files a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/mafft-profile and /dev/null differ diff --git a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/mafft.1 b/aphylogeo/bin/mafft-linux64/mafftdir/libexec/mafft.1 deleted file mode 100755 index b5344c57..00000000 --- a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/mafft.1 +++ /dev/null @@ -1,479 +0,0 @@ -.\" Title: MAFFT -.\" Author: Kazutaka Katoh -.\" Generator: DocBook XSL Stylesheets v1.72.0 -.\" Date: 2007-08-14 -.\" Manual: Mafft Manual -.\" Source: mafft 6.240 -.\" -.TH "MAFFT" "1" "2007\-06\-09" "mafft 6.240" "Mafft Manual" -.\" disable hyphenation -.nh -.\" disable justification (adjust text to left margin only) -.ad l -.SH "THIS MANUAL IS FOR V6.2XX (2007)" -Recent versions (v7.1xx; 2013 Jan.) have more features than those described below. -See also the tips page at -http://mafft.cbrc.jp/alignment/software/tips0.html -.SH "NAME" -.RS 0 -.sp -mafft \- Multiple alignment program for amino acid or nucleotide sequences -.RE -.SH "SYNOPSIS" -.RS 0 -.HP 6 -\fBmafft\fR [\fBoptions\fR] \fIinput\fR [>\ \fIoutput\fR] -.HP 6 -\fBlinsi\fR \fIinput\fR [>\ \fIoutput\fR] -.HP 6 -\fBginsi\fR \fIinput\fR [>\ \fIoutput\fR] -.HP 6 -\fBeinsi\fR \fIinput\fR [>\ \fIoutput\fR] -.HP 7 -\fBfftnsi\fR \fIinput\fR [>\ \fIoutput\fR] -.HP 6 -\fBfftns\fR \fIinput\fR [>\ \fIoutput\fR] -.HP 5 -\fBnwns\fR \fIinput\fR [>\ \fIoutput\fR] -.HP 6 -\fBnwnsi\fR \fIinput\fR [>\ \fIoutput\fR] -.HP 14 -\fBmafft\-profile\fR \fIgroup1\fR \fIgroup2\fR [>\ \fIoutput\fR] -.HP -.sp -\fIinput\fR, \fIgroup1\fR and \fIgroup2\fR must be in FASTA format. -.RE -.SH "DESCRIPTION" -.RS 0 -\fBMAFFT\fR is a multiple sequence alignment program for unix\-like operating systems. It offers a range of multiple alignment methods. -.SS "Accuracy\-oriented methods:" -.sp -.RS 4 -\h'-04'\(bu\h'+03'L\-INS\-i (probably most accurate; recommended for <200 sequences; iterative refinement method incorporating local pairwise alignment information): -.HP 6 -\fBmafft\fR \fB\-\-localpair\fR \fB\-\-maxiterate\fR\ \fI1000\fR \fIinput\fR [>\ \fIoutput\fR] -.HP 6 -\fBlinsi\fR \fIinput\fR [>\ \fIoutput\fR] -.RE -.sp -.RS 4 -\h'-04'\(bu\h'+03'G\-INS\-i (suitable for sequences of similar lengths; recommended for <200 sequences; iterative refinement method incorporating global pairwise alignment information): -.HP 6 -\fBmafft\fR \fB\-\-globalpair\fR \fB\-\-maxiterate\fR\ \fI1000\fR \fIinput\fR [>\ \fIoutput\fR] -.HP 6 -\fBginsi\fR \fIinput\fR [>\ \fIoutput\fR] -.RE -.sp -.RS 4 -\h'-04'\(bu\h'+03'E\-INS\-i (suitable for sequences containing large unalignable regions; recommended for <200 sequences): -.HP 6 -\fBmafft\fR \fB\-\-ep\fR\ \fI0\fR \fB\-\-genafpair\fR \fB\-\-maxiterate\fR\ \fI1000\fR \fIinput\fR [>\ \fIoutput\fR] -.HP 6 -\fBeinsi\fR \fIinput\fR [>\ \fIoutput\fR] -.br - -For E\-INS\-i, the -\fB\-\-ep\fR -\fI0\fR -option is recommended to allow large gaps. -.RE -.SS "Speed\-oriented methods:" -.sp -.RS 4 -\h'-04'\(bu\h'+03'FFT\-NS\-i (iterative refinement method; two cycles only): -.HP 6 -\fBmafft\fR \fB\-\-retree\fR\ \fI2\fR \fB\-\-maxiterate\fR\ \fI2\fR \fIinput\fR [>\ \fIoutput\fR] -.HP 7 -\fBfftnsi\fR \fIinput\fR [>\ \fIoutput\fR] -.RE -.sp -.RS 4 -\h'-04'\(bu\h'+03'FFT\-NS\-i (iterative refinement method; max. 1000 iterations): -.HP 6 -\fBmafft\fR \fB\-\-retree\fR\ \fI2\fR \fB\-\-maxiterate\fR\ \fI1000\fR \fIinput\fR [>\ \fIoutput\fR] -.RE -.sp -.RS 4 -\h'-04'\(bu\h'+03'FFT\-NS\-2 (fast; progressive method): -.HP 6 -\fBmafft\fR \fB\-\-retree\fR\ \fI2\fR \fB\-\-maxiterate\fR\ \fI0\fR \fIinput\fR [>\ \fIoutput\fR] -.HP 6 -\fBfftns\fR \fIinput\fR [>\ \fIoutput\fR] -.RE -.sp -.RS 4 -\h'-04'\(bu\h'+03'FFT\-NS\-1 (very fast; recommended for >2000 sequences; progressive method with a rough guide tree): -.HP 6 -\fBmafft\fR \fB\-\-retree\fR\ \fI1\fR \fB\-\-maxiterate\fR\ \fI0\fR \fIinput\fR [>\ \fIoutput\fR] -.RE -.sp -.RS 4 -\h'-04'\(bu\h'+03'NW\-NS\-i (iterative refinement method without FFT approximation; two cycles only): -.HP 6 -\fBmafft\fR \fB\-\-retree\fR\ \fI2\fR \fB\-\-maxiterate\fR\ \fI2\fR \fB\-\-nofft\fR\ \fIinput\fR [>\ \fIoutput\fR] -.HP 7 -\fBnwnsi\fR \fIinput\fR [>\ \fIoutput\fR] -.RE -.sp -.RS 4 -\h'-04'\(bu\h'+03'NW\-NS\-2 (fast; progressive method without the FFT approximation): -.HP 6 -\fBmafft\fR \fB\-\-retree\fR\ \fI2\fR \fB\-\-maxiterate\fR\ \fI0\fR \fB\-\-nofft\fR\ \fIinput\fR [>\ \fIoutput\fR] -.HP 6 -\fBnwns\fR \fIinput\fR [>\ \fIoutput\fR] -.RE -.sp -.RS 4 -\h'-04'\(bu\h'+03'NW\-NS\-PartTree\-1 (recommended for ~10,000 to ~50,000 sequences; progressive method with the PartTree algorithm): -.HP 6 -\fBmafft\fR \fB\-\-retree\fR\ \fI1\fR \fB\-\-maxiterate\fR\ \fI0\fR \fB\-\-nofft\fR\ \fB\-\-parttree\fR \fIinput\fR [>\ \fIoutput\fR] -.RE -.SS "Group\-to\-group alignments" -.HP 6 -.RS 4 -\fBmafft\-profile\fR \fIgroup1\fR \fIgroup2\fR [>\ \fIoutput\fR] -.sp -or: -.sp -\fBmafft\fR \fB\-\-maxiterate\fR\ \fI1000\fR \fB\-\-seed\fR\ \fIgroup1\fR \fB\-\-seed\fR\ \fIgroup2\fR /dev/null [>\ \fIoutput\fR] -.RE -.RE -.RE -.SH "OPTIONS" -.SS "Algorithm" -.RS 0 -.PP -\fB\-\-auto\fR -.RS 4 -Automatically selects an appropriate strategy from L\-INS\-i, FFT\-NS\-i and FFT\-NS\-2, according to data -size. Default: off (always FFT\-NS\-2) -.RE -.PP -\fB\-\-6merpair\fR -.RS 4 -Distance is calculated based on the number of shared 6mers. Default: on -.RE -.PP -\fB\-\-globalpair\fR -.RS 4 -All pairwise alignments are computed with the Needleman\-Wunsch -algorithm. More accurate but slower -than \-\-6merpair. Suitable for a set of -globally alignable sequences. Applicable to -up to ~200 sequences. A combination with \-\-maxiterate 1000 is recommended (G\-INS\-i). Default: off (6mer distance is used) -.RE -.PP -\fB\-\-localpair\fR -.RS 4 -All pairwise alignments are computed with the Smith\-Waterman -algorithm. More accurate but slower -than \-\-6merpair. Suitable for a set of -locally alignable sequences. Applicable to -up to ~200 sequences. A combination with \-\-maxiterate 1000 is recommended (L\-INS\-i). Default: off (6mer distance is used) -.RE -.PP -\fB\-\-genafpair\fR -.RS 4 -All pairwise alignments are computed with a local -algorithm with the generalized affine gap cost -(Altschul 1998). More accurate but slower -than \-\-6merpair. Suitable when large internal gaps -are expected. Applicable to -up to ~200 sequences. A combination with \-\-maxiterate 1000 is recommended (E\-INS\-i). Default: off (6mer distance is used) -.RE -.\".PP -.\"\fB\-\-fastswpair\fR -.\".RS 4 -.\"Distance is calculated based on a FASTA alignment. -.\"FASTA is required. Default: off (6mer distance is used) -.\".RE -.PP -\fB\-\-fastapair\fR -.RS 4 -All pairwise alignments are computed with FASTA (Pearson and Lipman 1988). -FASTA is required. Default: off (6mer distance is used) -.RE -.\".PP -.\"\fB\-\-blastpair\fR -.\".RS 4 -.\"Distance is calculated based on a BLAST alignment. BLAST is -.\"required. Default: off (6mer distance is used) -.\".RE -.PP -\fB\-\-weighti\fR \fInumber\fR -.RS 4 -Weighting factor for the consistency term calculated from pairwise alignments. Valid when -either of \-\-globalpair, \-\-localpair, \-\-genafpair, \-\-fastapair or -\-\-blastpair is selected. Default: 2.7 -.RE -.PP -\fB\-\-retree\fR \fInumber\fR -.RS 4 -Guide tree is built \fInumber\fR times in the -progressive stage. Valid with 6mer distance. Default: 2 -.RE -.PP -\fB\-\-maxiterate\fR \fInumber\fR -.RS 4 -\fInumber\fR cycles of iterative refinement are performed. Default: 0 -.RE -.PP -\fB\-\-fft\fR -.RS 4 -Use FFT approximation in group\-to\-group alignment. Default: on -.RE -.PP -\fB\-\-nofft\fR -.RS 4 -Do not use FFT approximation in group\-to\-group alignment. Default: off -.RE -.PP -\fB\-\-noscore\fR -.RS 4 -Alignment score is not checked in the iterative refinement stage. Default: off (score is checked) -.RE -.PP -\fB\-\-memsave\fR -.RS 4 -Use the Myers\-Miller (1988) algorithm. Default: automatically turned on when the alignment length exceeds 10,000 (aa/nt). -.RE -.PP -\fB\-\-parttree\fR -.RS 4 -Use a fast tree\-building method (PartTree, Katoh and Toh 2007) with -the 6mer distance. Recommended for a large number (> ~10,000) -of sequences are input. Default: off -.RE -.PP -\fB\-\-dpparttree\fR -.RS 4 -The PartTree algorithm is used with distances based on DP. Slightly -more accurate and slower than \-\-parttree. Recommended for a large -number (> ~10,000) of sequences are input. Default: off -.RE -.PP -\fB\-\-fastaparttree\fR -.RS 4 -The PartTree algorithm is used with distances based on FASTA. Slightly more accurate and slower than \-\-parttree. Recommended for a large number (> ~10,000) of sequences are input. FASTA is required. Default: off -.RE -.PP -\fB\-\-partsize\fR \fInumber\fR -.RS 4 -The number of partitions in the PartTree algorithm. Default: 50 -.RE -.PP -\fB\-\-groupsize\fR \fInumber\fR -.RS 4 -Do not make alignment larger than \fInumber\fR sequences. Valid only with the \-\-*parttree options. Default: the number of input sequences -.RE -.RE -.SS "Parameter" -.RS 0 -.PP -\fB\-\-op\fR \fInumber\fR -.RS 4 -Gap opening penalty at group\-to\-group alignment. Default: 1.53 -.RE -.PP -\fB\-\-ep\fR \fInumber\fR -.RS 4 -Offset value, which works like gap extension penalty, for -group\-to\-group alignment. Default: 0.123 -.RE -.PP -\fB\-\-lop\fR \fInumber\fR -.RS 4 -Gap opening penalty at local pairwise -alignment. Valid when -the \-\-localpair or \-\-genafpair option is selected. Default: \-2.00 -.RE -.PP -\fB\-\-lep\fR \fInumber\fR -.RS 4 -Offset value at local pairwise alignment. Valid when -the \-\-localpair or \-\-genafpair option is selected. Default: 0.1 -.RE -.PP -\fB\-\-lexp\fR \fInumber\fR -.RS 4 -Gap extension penalty at local pairwise alignment. Valid when -the \-\-localpair or \-\-genafpair option is selected. Default: \-0.1 -.RE -.PP -\fB\-\-LOP\fR \fInumber\fR -.RS 4 -Gap opening penalty to skip the alignment. Valid when the -\-\-genafpair option is selected. Default: \-6.00 -.RE -.PP -\fB\-\-LEXP\fR \fInumber\fR -.RS 4 -Gap extension penalty to skip the alignment. Valid when the -\-\-genafpair option is selected. Default: 0.00 -.RE -.PP -\fB\-\-bl\fR \fInumber\fR -.RS 4 -BLOSUM \fInumber\fR matrix (Henikoff and Henikoff 1992) is used. \fInumber\fR=30, 45, 62 or 80. Default: 62 -.RE -.PP -\fB\-\-jtt\fR \fInumber\fR -.RS 4 -JTT PAM \fInumber\fR (Jones et al. 1992) matrix is used. \fInumber\fR>0. Default: BLOSUM62 -.RE -.PP -\fB\-\-tm\fR \fInumber\fR -.RS 4 -Transmembrane PAM \fInumber\fR (Jones et al. 1994) matrix is used. \fInumber\fR>0. Default: BLOSUM62 -.RE -.PP -\fB\-\-aamatrix\fR \fImatrixfile\fR -.RS 4 -Use a user\-defined AA scoring matrix. The format of \fImatrixfile\fR is -the same to that of BLAST. Ignored when nucleotide sequences are input. Default: BLOSUM62 -.RE -.PP -\fB\-\-fmodel\fR -.RS 4 -Incorporate the AA/nuc composition information into -the scoring matrix. Default: off -.RE -.RE -.SS "Output" -.RS 0 -.PP -\fB\-\-clustalout\fR -.RS 4 -Output format: clustal format. Default: off (fasta format) -.RE -.PP -\fB\-\-inputorder\fR -.RS 4 -Output order: same as input. Default: on -.RE -.PP -\fB\-\-reorder\fR -.RS 4 -Output order: aligned. Default: off (inputorder) -.RE -.PP -\fB\-\-treeout\fR -.RS 4 -Guide tree is output to the \fIinput\fR.tree file. Default: off -.RE -.PP -\fB\-\-quiet\fR -.RS 4 -Do not report progress. Default: off -.RE -.RE -.SS "Input" -.RS 0 -.PP -\fB\-\-nuc\fR -.RS 4 -Assume the sequences are nucleotide. Default: auto -.RE -.PP -\fB\-\-amino\fR -.RS 4 -Assume the sequences are amino acid. Default: auto -.RE -.PP -\fB\-\-seed\fR \fIalignment1\fR [\fB--seed\fR \fIalignment2\fR \fB--seed\fR \fIalignment3\fR ...] -.RS 4 -Seed alignments given in \fIalignment_n\fR (fasta format) are aligned with -sequences in \fIinput\fR. The alignment within every seed is preserved. -.RE -.RE -.SH "FILES" -.RS 0 -.PP -Mafft stores the input sequences and other files in a temporary directory, which by default is located in -\fI/tmp\fR. -.RE -.SH "ENVIONMENT" -.RS 0 -.PP -\fBMAFFT_BINARIES\fR -.RS 4 -Indicates the location of the binary files used by mafft. By default, they are searched in -\fI/usr/local/lib/mafft\fR, but on Debian systems, they are searched in -\fI/usr/lib/mafft\fR. -.RE -.PP -\fBFASTA_4_MAFFT\fR -.RS 4 -This variable can be set to indicate to mafft the location to the fasta34 program if it is not in the PATH. -.RE -.RE -.SH "SEE ALSO" -.RS 0 -.PP - -\fBmafft\-homologs\fR(1) -.RE -.SH "REFERENCES" -.RS 0 -.SS "In English" -.sp -.RS 4 -\h'-04'\(bu\h'+03'Katoh and Toh (Bioinformatics 23:372\-374, 2007) PartTree: an algorithm to build an approximate tree from a large number of unaligned sequences (describes the PartTree algorithm). -.RE -.sp -.RS 4 -\h'-04'\(bu\h'+03'Katoh, Kuma, Toh and Miyata (Nucleic Acids Res. 33:511\-518, 2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment (describes [ancestral versions of] the G\-INS\-i, L\-INS\-i and E\-INS\-i strategies) -.RE -.sp -.RS 4 -\h'-04'\(bu\h'+03'Katoh, Misawa, Kuma and Miyata (Nucleic Acids Res. 30:3059\-3066, 2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform (describes the FFT\-NS\-1, FFT\-NS\-2 and FFT\-NS\-i strategies) -.RE -.SS "In Japanese" -.sp -.RS 4 -\h'-04'\(bu\h'+03'Katoh and Misawa (Seibutsubutsuri 46:312\-317, 2006) Multiple Sequence Alignments: the Next Generation -.RE -.sp -.RS 4 -\h'-04'\(bu\h'+03'Katoh and Kuma (Kagaku to Seibutsu 44:102\-108, 2006) Jissen\-teki Multiple Alignment -.RE -.RE -.SH "AUTHORS" -.RS 0 -.PP -\fBKazutaka Katoh\fR <\&kazutaka.katoh_at_aist.go.jp\&> -.sp -1n -.IP "" 4 -Wrote Mafft. -.PP -\fBCharles Plessy\fR <\&charles\-debian\-nospam_at_plessy.org\&> -.sp -1n -.IP "" 4 -Wrote this manpage in DocBook XML for the Debian distribution, using Mafft's homepage as a template. -.RE -.SH "COPYRIGHT" -.RS 0 -Copyright \(co 2002\-2007 Kazutaka Katoh (mafft) -.br -Copyright \(co 2007 Charles Plessy (this manpage) -.br -.PP -Mafft and its manpage are offered under the following conditions: -.PP -Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: -.sp -.RS 4 -\h'-04' 1.\h'+02'Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. -.RE -.sp -.RS 4 -\h'-04' 2.\h'+02'Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. -.RE -.sp -.RS 4 -\h'-04' 3.\h'+02'The name of the author may not be used to endorse or promote products derived from this software without specific prior written permission. -.RE -.PP -THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -.br -.RE diff --git a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/mafftash_premafft.pl b/aphylogeo/bin/mafft-linux64/mafftdir/libexec/mafftash_premafft.pl deleted file mode 100755 index 6dc3b9c4..00000000 --- a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/mafftash_premafft.pl +++ /dev/null @@ -1,464 +0,0 @@ -#!/usr/bin/perl - -##################################################################### -# Author: KM Amada (kmamada@ifrec.osaka-u.ac.jp) -# -# Ver. Date Changelog -##################################################################### -# 1.0 07.26.13 Initial release -# 2.0 09.03.13 Added extensive warnings and error messages -# 3.0 10.28.13 Fix for retrieving large files. Added STDERR logs -# 3.1 11.08.13 Added LWP failsafe. Made hat3 not a required output -# 3.2 12.08.14 Removed 5-char restriction for own structure files -# -##################################################################### - -use strict; -use Getopt::Long; -use File::Path qw(make_path remove_tree); -use LWP::Simple; -use LWP::UserAgent; - -# to prevent error 'Header line too long (limit is 8192)' [v3.1] -use LWP::Protocol::http; -push(@LWP::Protocol::http::EXTRA_SOCK_OPTS, MaxLineLength => 0); - - - -my $BASEURL = "http://sysimm.ifrec.osaka-u.ac.jp/MAFFTash/REST/service.cgi/premafft"; - -my ( $WORKDIR, $PDBLIST, $OWNLIST, $HAT3FILE, $INSTRFILE ); - -GetOptions -( - 'd=s' => \$WORKDIR, - 'p=s' => \$PDBLIST, - 'o=s' => \$OWNLIST, - 'h=s' => \$HAT3FILE, - 'i=s' => \$INSTRFILE, -); - -print STDERR "[MAFFTash-premafft]\n"; - -# set temp directory -my $TMP = "/tmp/mapremafft$$"; -make_path($TMP) unless -d $TMP; - - - -###### -# validation -&help("Required parameter : atleast one of either '-p' or '-o'") unless ( defined $PDBLIST || defined $OWNLIST); -&help("Required parameter : '-d'") if defined $OWNLIST && ! defined $WORKDIR; - -$HAT3FILE = "hat3" unless defined $HAT3FILE; -$INSTRFILE = "instr" unless defined $INSTRFILE; -chop $WORKDIR if defined $WORKDIR && $WORKDIR =~ m/\/$/g; - - -###### -# prepare inputs -print STDERR "Preparing inputs for service request...\n"; - -my @files = (); -push(@files, "strweight" => "0.5"); -push(@files, "premafft" => "1"); - - -# pdb entries -if ( defined $PDBLIST ) -{ - print STDERR "PDB List defined!\n"; - &bail("Error: Input file $PDBLIST does not exists!") unless -e $PDBLIST; - my $listfile = "$TMP/pdblist.inp"; - - - open(INPF,"<$PDBLIST") or &bail("Error: Cannot open file $PDBLIST for reading!"); - open(OUTF,">$listfile") or &bail("Error: Cannot open temporary file $listfile for writing!"); - - while() - { - chomp; - if ( /^(\w{5})$/ ) - { - print OUTF ">PDBID\n$1\n"; - } - } - - close OUTF; - close INPF; - - push(@files, "inputfile" => ["$listfile"]); -} - - - -# upload own structures -my %ownids = (); - -if ( defined $OWNLIST ) -{ - print STDERR "OWN List defined!\n"; - &bail("Error: Input file $OWNLIST does not exists!") unless -e $OWNLIST; - - - open(OWNINPF,"<$OWNLIST") or &bail("Error: Cannot open file $OWNLIST for reading!"); - - while() - { - chomp; - - if ( /^(\S+)$/ ) - { - my $fileref = "$WORKDIR/$1.pdb"; - - unless (-e $fileref) - { - close OWNINPF; - &bail("Error: File $fileref does not exists!"); - } - - push(@files, "inputownfile[]" => ["$fileref"]); - $ownids{$1} = 1; - } - } - - close OWNINPF; -} - - - -###### -# start rest service -print STDERR "Sending service request...\n"; - -my $browser = LWP::UserAgent->new; -$browser->timeout(0); - - -# post: running a mafftash job -my $postResponse = $browser->post( $BASEURL, \@files, 'Content_Type' => 'form-data' ); -&bail(sprintf("[%d] %s\n", $postResponse->code, &parseError($postResponse->content))) unless($postResponse->is_success); - - -# get response from post request -my ($status, $mafftashid) = &parseResponse($postResponse->content); - - - -my $MAXTRIES = 3; -my $STIMER = 4; -my $longtimer = 0; - -print STDERR "Request sent! Waiting for response...[$mafftashid]\n"; - - -# wait for results until it becomes available -while(1) -{ - $longtimer = $longtimer <= ($STIMER*3) ? $longtimer+$STIMER : $STIMER; - sleep $longtimer; - - - # get: get results for mafftash job - my $getResponse = $browser->get("$BASEURL/$mafftashid"); - - if ( $getResponse->is_success ) - { - - # get response from get request - ($status, $mafftashid) = &parseResponse($getResponse->content); - next unless ( $status eq "done" ); - - - # if job is finished and ready - print STDERR "Results found!\n"; - my $csfile = "$TMP/checksum.tar.gz"; - my $try1 = 1; - - - while(1) - { - print STDERR "Fetching Results... [Trial $try1]\n"; - - if ( is_success(getstore("$BASEURL/getmdlist/$mafftashid", $csfile)) && -e $csfile && -s $csfile ) - { - # get response from get request - my $checklist = &extractchecksum($csfile); - &bail("Error retrieving list of compressed files!") unless ( scalar %$checklist > 0 ); - - - foreach my $id ( keys %$checklist ) - { - my $checkfile = "$TMP/$id"; - my $checkid = $checklist->{$id}; - my $try2 = 1; - - while(1) - { - unlink $checkfile if -e $checkfile; - - if ( is_success(getstore("$BASEURL/get/$mafftashid/$id", $checkfile)) && -e $checkfile && -s $checkfile ) - { - my $hashid = &getchecksum($checkfile); - #print STDERR "[hashid]$hashid [checkid]$checkid\n"; - - if ($hashid ne "" && $hashid ne $checkid ) - { - unlink $checkfile if -e $checkfile; - &bail("Error retrieving compressed file from server! [Checksum Failed]") if $try2 >= $MAXTRIES; - $try2++; - sleep $STIMER; - } - else - { - last; - } - } - else - { - &bail("Error retrieving compressed file from server!") if $try2 >= $MAXTRIES; - $try2++; - sleep $STIMER; - } - } - } - - last; - } - else - { - &bail("Error retrieving list of compressed files from server!") if $try1 >= $MAXTRIES; - $try1++; - sleep $STIMER; - } - } - - last; - - } - else - { - &bail(sprintf("[%d] %s\n", $getResponse->code, &parseError($getResponse->content))); - } - -} - - -# make sure outputs were generated -# decompress -print STDERR "Assembling final results...\n"; - -&backticks("cat $TMP/archive.tar.gz* | tar -zxf - -C $TMP/"); -&backticks("mv -f $TMP/instr $INSTRFILE") if -e "$TMP/instr"; -&backticks("mv -f $TMP/hat3 $HAT3FILE") if -e "$TMP/hat3"; - -# sometimes no hat3 file is generated [v3.1] -#&bail("Error: Output file $HAT3FILE not found!") unless -e $HAT3FILE; -&bail("Error: Output file $INSTRFILE not found!") unless -e $INSTRFILE; - - -# warn if some ownids were ommitted -if ( scalar keys(%ownids) > 0 ) -{ - my %instrids = (); - - open(INSTRF,"<$INSTRFILE") or &bail("Error: Cannot open file $INSTRFILE for reading!"); - - while() - { - chomp; - - if ( /^>\d+_(\S+)$/ ) - { - $instrids{$1} = 1; - } - } - - close INSTRF; - - foreach my $id ( keys %ownids ) - { - warn "Warning: Own structure $id was excluded from instr/hat3.\n" unless $instrids{$id}; - } - -} - - - -&cleanup(); - - - -#################### -#################### - - - -sub parseResponse -{ - my $response = shift; - - #"status":"wait","mafftashid":"Ma8211432R" - - my $status = ""; - my $mafftashid = ""; - - if ( $response =~ /^([^\s:]+):([^\s:]+)$/ ) - { - $mafftashid = $1; - $status = $2; - } - - return ($status, $mafftashid); - -} - - -sub extractchecksum -{ - my $infile = shift; - my %dataset = (); - - open CSUM, "tar -zxf $infile -O|" or return \%dataset; - - while() - { - chomp; - if ( /^(\S+)\s+(\S+)$/ ) - { - $dataset{$2} = $1; - } - - } - - close CSUM; - - return \%dataset; - -} - - -sub parseError -{ - my $response = shift; - - #"error":"Invalid number of inputs found." - my $errorstr = ( $response =~ /\"error\"\s*:\s*\"([^\"]+)\"/ ) ? $1 : ""; - return $errorstr; -} - - -sub getchecksum -{ - my $infile = shift; - - # md5 binary check - my $MD5BIN = ""; - - if ( -x "/usr/bin/md5sum" ) - { - $MD5BIN = "/usr/bin/md5sum"; - } - elsif ( -x "/sbin/md5" ) - { - $MD5BIN = "/sbin/md5 -q"; - } - - return "" if $MD5BIN eq ""; - - - my $checksum = ""; - open MD5EXE, "$MD5BIN $infile|" or return ""; - - while() - { - if (/^(\S+)\s+(\S+)$/) - { - $checksum = $1; - last; - } - elsif (/^(\S+)$/) - { - $checksum = $1; - last; - } - } - - close MD5EXE; - - return $checksum; - -} - - -sub backticks -{ - my $command = shift; - - `$command`; - return ($? == -1) ? 0 : 1; -} - - -sub bail -{ - my $str = shift; - print STDERR "$str\n" if defined $str; - - &cleanup(); - exit(1); -} - - -sub cleanup -{ - return if ($TMP eq "" || !-d $TMP); - - opendir(MAINDIR, $TMP); - my @files = readdir(MAINDIR); - closedir(MAINDIR); - - foreach my $file (@files) - { - unlink "$TMP/$file" if -e "$TMP/$file"; - } - - remove_tree($TMP); - -} - - -sub help -{ - my $str = shift; - - print <<'HELPME'; - -USAGE - ./mafftash_premafft.pl -p [FILE] - ./mafftash_premafft.pl -o [FILE] -d [DIRECTORY] - ./mafftash_premafft.pl -p [FILE] -o [FILE] -d [DIRECTORY] - - -PARAMETERS - -p [FILE] - FILE contains a list of PDBIDs (one entry per line); make sure that the PDBIDs are in the standard 5-character pdbid+chain naming format - - -o [FILE] -d [DIRECTORY] - FILE contains a list of IDs from your own structure/pdb files (one entry per line) - for each ID in the list make sure that a corresponding structure file (same ID with .pdb extension) is stored in DIRECTORY - - -h [HATFILE] - save the output hat3 file in HATFILE; if not set, the output is written to a file named 'hat3' in your current directory - - -i [INSTRFILE] - save the output instr file in INSTRFILE; if not set, the output is written to a file named 'instr' in your current directory - -HELPME - - &bail($str); -} - - - diff --git a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/maffttext2hex b/aphylogeo/bin/mafft-linux64/mafftdir/libexec/maffttext2hex deleted file mode 100755 index ac2ad2c6..00000000 Binary files a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/maffttext2hex and /dev/null differ diff --git a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/makedirectionlist b/aphylogeo/bin/mafft-linux64/mafftdir/libexec/makedirectionlist deleted file mode 100755 index 4306f59a..00000000 Binary files a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/makedirectionlist and /dev/null differ diff --git a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/mccaskillwrap b/aphylogeo/bin/mafft-linux64/mafftdir/libexec/mccaskillwrap deleted file mode 100755 index 40e7163d..00000000 Binary files a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/mccaskillwrap and /dev/null differ diff --git a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/multi2hat3s b/aphylogeo/bin/mafft-linux64/mafftdir/libexec/multi2hat3s deleted file mode 100755 index 048ba0d8..00000000 Binary files a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/multi2hat3s and /dev/null differ diff --git a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/nodepair b/aphylogeo/bin/mafft-linux64/mafftdir/libexec/nodepair deleted file mode 100755 index fedb250b..00000000 Binary files a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/nodepair and /dev/null differ diff --git a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/pairash b/aphylogeo/bin/mafft-linux64/mafftdir/libexec/pairash deleted file mode 100755 index a3a425c4..00000000 Binary files a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/pairash and /dev/null differ diff --git a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/pairlocalalign b/aphylogeo/bin/mafft-linux64/mafftdir/libexec/pairlocalalign deleted file mode 100755 index fca217c6..00000000 Binary files a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/pairlocalalign and /dev/null differ diff --git a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/regtable2seq b/aphylogeo/bin/mafft-linux64/mafftdir/libexec/regtable2seq deleted file mode 100755 index ded9bd6a..00000000 Binary files a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/regtable2seq and /dev/null differ diff --git a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/replaceu b/aphylogeo/bin/mafft-linux64/mafftdir/libexec/replaceu deleted file mode 100755 index a815e28e..00000000 Binary files a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/replaceu and /dev/null differ diff --git a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/restoreu b/aphylogeo/bin/mafft-linux64/mafftdir/libexec/restoreu deleted file mode 100755 index e0a984be..00000000 Binary files a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/restoreu and /dev/null differ diff --git a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/score b/aphylogeo/bin/mafft-linux64/mafftdir/libexec/score deleted file mode 100755 index 7be34007..00000000 Binary files a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/score and /dev/null differ diff --git a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/seekquencer_premafft.pl b/aphylogeo/bin/mafft-linux64/mafftdir/libexec/seekquencer_premafft.pl deleted file mode 100755 index a9040fdd..00000000 --- a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/seekquencer_premafft.pl +++ /dev/null @@ -1,600 +0,0 @@ -#!/usr/bin/perl - -#################################################################################### -# Author: KM Amada (kmamada@ifrec.osaka-u.ac.jp) -# -# Ver. Date Changelog -#################################################################################### -# 1.0 11.01.13 Initial release -# -# **Skipped version 2 to standardise version numbers to seekquencer.pl script** -# -# 3.0 04.24.14 Added split option -mod for output -# Uses seekquencer_v3 backend -# -# 4.0 05.12.14 Added new options: -run -trd -noin -# Sets -seqa fast in seekquencer.pl -# Uses seekquencer_v4 backend -# -# 4.1 05.19.14 Added a check on running REST requests before proceeding -# to avoid server load problems -# -# 4.2 05.27.14 Seq limit processing done in seekquencer.pl script -# to avoid server load problems -# -# 4.3 07.22.14 Added new option: -seqd -# Blast limit changed from factor of 10 to -blim option -# Timing on sleep changed; added srand() for making seed -# Moved the job limit processing to server side -# -# 4.4 08.05.14 Modified to work in multiple OS -# -# -#################################################################################### - -use strict; -use Getopt::Long; -use File::Path qw(make_path remove_tree); -use Cwd; -use LWP::Simple; -use LWP::UserAgent; - -# to prevent error: Header line too long (limit is 8192) -use LWP::Protocol::http; -push(@LWP::Protocol::http::EXTRA_SOCK_OPTS, MaxLineLength => 0); - - - -my $BASEURL = "http://sysimm.ifrec.osaka-u.ac.jp/seekquencer/REST/service.cgi/premafft"; -my ( $INPUTFILE, $IDLISTFILE, $SEQFASTAFILE, $OUTPUTFILE, $SEQFLAG, $STRFLAG, $EVALFLAG, $NOINFLAG ); -my $OUTTYPE = "mafftash"; - -my $SEQDATABASE = "uniref100"; -my $SEQLIMIT = 100; -my $SEQBLASTLIMIT = 100; - -my $RUNMODE = "normal"; # thread|normal -my $THREADCOUNT = 3; - - -GetOptions -( - 'inp=s' => \$INPUTFILE, - 'idf=s' => \$IDLISTFILE, - 'seqf=s' => \$SEQFASTAFILE, - 'out=s' => \$OUTPUTFILE, - 'str' => \$STRFLAG, - 'seq' => \$SEQFLAG, - 'seqd=s' => \$SEQDATABASE, - 'lim=i' => \$SEQLIMIT, - 'blim=i' => \$SEQBLASTLIMIT, - 'pre' => \$EVALFLAG, - 'noin' => \$NOINFLAG, - 'mod=s' => \$OUTTYPE, - 'run=s' => \$RUNMODE, - 'trd=i' => \$THREADCOUNT, - - -); - -my $ISWINDOWS = ( $^O =~ /^MSWin/ ) ? 1 : 0; -print STDERR "[Seekquencer-premafft 4.4 on $^O]\n"; - - -# set temp directory -my $CWD = getcwd; -my $TMP = "$CWD/seekpremafft$$"; -make_path($TMP) unless -d $TMP; - - - -###### -# validation -help("Required parameter: define input as '-inp' or '-idf' or '-seqf'") if ( !defined $INPUTFILE && !defined $IDLISTFILE && !defined $SEQFASTAFILE ); -help("'-inp' is already defined") if ( defined $INPUTFILE && (defined $IDLISTFILE || defined $SEQFASTAFILE) ); -help("Input file $INPUTFILE does not exist (or filesize is 0)") if ( defined $INPUTFILE && (! -e $INPUTFILE || !-s $INPUTFILE) ); -help("Input file $IDLISTFILE does not exist (or filesize is 0)") if ( defined $IDLISTFILE && (! -e $IDLISTFILE || !-s $IDLISTFILE) ); -help("Input file $SEQFASTAFILE does not exist (or filesize is 0)") if ( defined $SEQFASTAFILE && (! -e $SEQFASTAFILE || !-s $SEQFASTAFILE) ); -help("Required parameter: output file '-out'") unless ( defined $OUTPUTFILE ); -help("Set either '-str' or '-seq' or dont set any at all") if ( defined $STRFLAG && defined $SEQFLAG ); - -help("Invalid value for '-seqd '") if ( $SEQDATABASE ne "uniref100" && $SEQDATABASE ne "uniref90" && $SEQDATABASE ne "uniref70" && $SEQDATABASE ne "uniprot"); -help("Invalid value for '-mod '") if ( $OUTTYPE ne "fasta" && $OUTTYPE ne "mafftash" && $OUTTYPE ne "mafftash-split" ); -help("Invalid value for '-run '") if ( $RUNMODE ne "thread" && $RUNMODE ne "normal" ); -help("Invalid value for '-trd '; count should be between 1 and 5 (inclusive)") if ( $RUNMODE eq "thread" && ($THREADCOUNT <= 0 || $THREADCOUNT > 5) ); - - -###### -# check existing requests -print STDERR "Checking server status...\n"; - -# generate seed -srand($$); - -# sleep a bit to give time for lsf response -sleep(int(rand(6))+1); - - -my $browser = LWP::UserAgent->new; -$browser->timeout(0); - -# get: check if you can send a new request this time -my $jobsResponse = $browser->get("$BASEURL/isAllowed"); - -if ( $jobsResponse->is_success ) -{ - my $status = parseJobQueryResponse($jobsResponse->content); - bail("Max jobs reached. The server cannot process your request right now; try again later.", 0) unless $status > 0; -} -else -{ - bail(sprintf("[%d] %s\n", $jobsResponse->code, parseError($jobsResponse->content))); -} - - -###### -# make a temporary input if lists were provided -unless ( defined $INPUTFILE ) -{ - $INPUTFILE = "$TMP/input.homemade"; - open INPF, ">$INPUTFILE" or bail("Error writing to input file."); - - if ( defined $IDLISTFILE ) - { - open IDLIST, "<$IDLISTFILE" or bail("Error reading input file."); - while( ) - { - chomp; - if ( /(\w{5})/ ) - { - print INPF ">PDBID\n$1\n"; - } - } - close IDLIST; - } - - - if ( defined $SEQFASTAFILE ) - { - open FASTA, "<$SEQFASTAFILE" or bail("Error reading input file."); - while( ) - { - chomp; - print INPF "$_\n"; - } - close FASTA; - } - - close INPF; -} - - -###### -# prepare parameters -print STDERR "Preparing parameters for service request...\n"; - -my @parameters = (); -push(@parameters, "fileinput" => ["$INPUTFILE"]); -push(@parameters, "out_type" => $OUTTYPE); - -push(@parameters, "rest_flag" => "1"); -push(@parameters, "cls_flag" => "1"); -push(@parameters, "pre_flag" => "1") if defined $EVALFLAG; -push(@parameters, "noin_flag" => "1") if defined $NOINFLAG; - -push(@parameters, "run_mode" => $RUNMODE); -push(@parameters, "thread_count" => $THREADCOUNT) if $RUNMODE eq "thread"; - - -if ( defined $STRFLAG ) -{ - push(@parameters, "str_flag" => "1"); - push(@parameters, "ash_flag" => "1"); -} -elsif ( defined $SEQFLAG ) -{ - push(@parameters, "seq_flag" => "1"); - push(@parameters, "seq_algorithm" => "fast"); - push(@parameters, "seq_database" => $SEQDATABASE); - push(@parameters, "seq_blastlimit" => $SEQBLASTLIMIT); - push(@parameters, "seq_outputlimit" => $SEQLIMIT); -} -else -{ - push(@parameters, "str_flag" => "1"); - push(@parameters, "ash_flag" => "1"); - push(@parameters, "seq_flag" => "1"); - push(@parameters, "seq_algorithm" => "fast"); - push(@parameters, "seq_database" => $SEQDATABASE); - push(@parameters, "seq_blastlimit" => $SEQBLASTLIMIT); - push(@parameters, "seq_outputlimit" => $SEQLIMIT); -} - - - -###### -# start rest service -print STDERR "Sending service request...\n"; - -# post: running a mafftash job -my $postResponse = $browser->post( $BASEURL, \@parameters, 'Content_Type' => 'form-data' ); -bail(sprintf("[%d] %s\n", $postResponse->code, parseError($postResponse->content))) unless($postResponse->is_success); - - -# get response from post request -my ($status, $seekid) = parseResponse($postResponse->content); - -my $MAXTRIES = 3; -my $STIMER = 5; -my $timer = 0; - -print STDERR "Request sent! Waiting for response...[$seekid]\n"; - -my $checklist = {}; - -# wait for results until it becomes available -while(1) -{ - # sleeps for 5+random, 10+random, 15+random, 20+random, 25+random, 30+random ,,, 60+random, 60+random,,, - $timer = $timer >= 60 ? 60 : $timer+$STIMER; - sleep($timer+int(rand(4))); - - # get: get results for mafftash job - my $getResponse = $browser->get("$BASEURL/$seekid"); - - if ( $getResponse->is_success ) - { - - # get response from get request - ($status, $seekid) = parseResponse($getResponse->content); - next unless ( $status eq "done" ); - - - # if job is finished and ready - print STDERR "Results found!\n"; - my $csfile = "$TMP/checksum"; - my $try1 = 1; - - - while(1) - { - print STDERR "Fetching Results... [Trial $try1]\n"; - - if ( is_success(getstore("$BASEURL/get/$seekid/checksum", $csfile)) && -e $csfile && -s $csfile ) - { - # get response from get request - $checklist = extractchecksum($csfile); - bail("Error retrieving list of compressed files!") unless ( scalar %$checklist > 0 ); - - - foreach my $id ( sort keys %$checklist ) - { - sleep 1; - my $checkfile = "$TMP/$id"; - my $checkid = $checklist->{$id}; - my $try2 = 1; - - while(1) - { - unlink $checkfile if -e $checkfile; - - if ( is_success(getstore("$BASEURL/get/$seekid/$id", $checkfile)) && -e $checkfile && -s $checkfile ) - { - last if $ISWINDOWS; - - my $hashid = getchecksum($checkfile); - #print STDERR "[hashid]$hashid [checkid]$checkid\n"; - - if ($hashid ne "" && $hashid ne $checkid ) - { - #unlink $checkfile if -e $checkfile; - bail("Error retrieving compressed file from server! [Checksum Failed]") if $try2 >= $MAXTRIES; - $try2++; - sleep $STIMER; - } - else - { - last; - } - } - else - { - bail("Error retrieving compressed file from server!") if $try2 >= $MAXTRIES; - $try2++; - sleep $STIMER; - } - } - } - - last; - } - else - { - bail("Error retrieving list of compressed files from server!") if $try1 >= $MAXTRIES; - $try1++; - sleep $STIMER; - } - } - - last; - - } - else - { - bail(sprintf("[%d] %s\n", $getResponse->code, parseError($getResponse->content))); - } - -} - - -# make sure outputs were generated -# decompress -print STDERR "Assembling final results...\n"; - -foreach my $id ( sort keys %$checklist ) -{ - if ( $id =~ /^$seekid\.out(\.str|\.seq)?/ ) - { - bail("Error: Output file corrupted!") unless -e "$TMP/$id"; - appendToFile("$TMP/$id","$OUTPUTFILE".$1); - } -} - -cleanup(); - - - -#################### -#################### - - -sub parseResponse -{ - my $response = shift; - my $status = ""; - my $seekid = ""; - - if ( $response =~ /^([^\s:]+):([^\s:]+)$/ ) - { - $seekid = $1; - $status = $2; - } - - return ($status, $seekid); -} - - -sub parseJobQueryResponse -{ - my $response = shift; - my $jobs = 100; - - if ( $response =~ /^(\d+)$/ ) - { - $jobs = $1; - } - - return $jobs; -} - - -sub extractchecksum -{ - my $infile = shift; - my %dataset = (); - - #open CSUM, "tar -zxf $infile -O|" or return \%dataset; - open CSUM, "<$infile" or return \%dataset; - - while() - { - chomp; - if ( /^(\S+)\s+(\S+)$/ ) - { - $dataset{$2} = $1; - } - } - - close CSUM; - - return \%dataset; -} - - -sub parseError -{ - my $response = shift; - - #"error":"Invalid number of inputs found." - my $errorstr = ( $response =~ /\"error\"\s*:\s*\"([^\"]+)\"/ ) ? $1 : $response; - return $errorstr; -} - - -sub getchecksum -{ - my $infile = shift; - - # md5 binary check - my $MD5BIN = ""; - - if ( -x "/usr/bin/md5sum" ) - { - $MD5BIN = "/usr/bin/md5sum"; - } - elsif ( -x "/sbin/md5" ) - { - $MD5BIN = "/sbin/md5 -q"; - } - - return "" if $MD5BIN eq ""; - - - my $checksum = ""; - open MD5EXE, "$MD5BIN $infile|" or return ""; - - while() - { - if (/^(\S+)\s+(\S+)$/) - { - $checksum = $1; - last; - } - elsif (/^(\S+)$/) - { - $checksum = $1; - last; - } - } - - close MD5EXE; - - return $checksum; - -} - - -sub backticks -{ - my $command = shift; - - `$command`; - return ($? == -1) ? 0 : 1; -} - - -sub bail -{ - my $str = shift; - my $status = shift; - - #0 for success and 1 for error - $status = 1 unless defined; - - print STDERR "$str\n" if defined $str; - - cleanup(); - - exit($status); -} - - -sub cleanup -{ - return if ($TMP eq "" || !-d $TMP); - - opendir(MAINDIR, $TMP); - my @files = readdir(MAINDIR); - closedir(MAINDIR); - - foreach my $file (@files) - { - unlink "$TMP/$file" if -e "$TMP/$file"; - } - - remove_tree($TMP); - -} - - -sub appendToFile -{ - my $inpfile = shift; - my $outfile = shift; - - open INPF, "<$inpfile" or bail("Server Error: Error in reading file."); - open OUTF, ">>$outfile" or bail("Server Error: Error in writing to file."); - - while() - { - print OUTF $_; - } - - close OUTF; - close INPF; -} - - - -sub help -{ - my $str = shift; - - print <<'HELPME'; - -USAGE - ./seekquencer_premafft.pl -inp -out [-str|-seq] - ./seekquencer_premafft.pl -idf -seqf -out [-str|-seq] - - -PARAMETERS - -inp - INFILE is a FASTA-formatted file - PDB entries are written as: - >PDBID - [5-character pdbid+chain] - - While sequence entries are written as: - >[id] - [sequence] - - -idf - IDLISTFILE is a file containing a list of pdbids - pdbids should be a 5-character pdbid + chain - - -seqf - SEQFASTA is a fasta file - entries are written as: - >[id] - [sequence] - - -out - Results are writen to a file named OUTFILE - - -str - Only structures will be collected by Seekquencer - If neither -str nor -seq is set, both structures and sequences will be collected by Seekquencer - - -seq - Only sequences will be collected by Seekquencer - If neither -str nor -seq is set, both structures and sequences will be collected by Seekquencer - - -OPTIONAL PARAMETERS: - -seqd - Search Database for sequence homologs. Default value: uniref100 - - -lim - this sets the maximum number of sequence homologs collected. Default value: 100 - - -blim - this sets the -b and -v value when running blastall. Default value: 100 - - -pre - When -str is set, this will compare all structures against all using pdp-ash - This would ensure that all structures collected are matching - All structures that do not match will be removed - - -noin - When set, inputs will not be included in the output - - -mod - Defines the output format - mafftash (default) will print a mafftash-formatted fasta file - mafftash-split will make 2 files separating the structures (OUTFILE.str) from sequences (OUTFILE.seq) - fasta will print a regular fasta file - - -run - thread will run simultaneous jobs during blast queries (faster but takes more nodes) - normal will run sequential blast queries (slower but takes less nodes) - Default value: normal - - -trd - if -run is defined, this sets the number of parallel jobs to run. Default value: 3 - - -HELPME - - bail($str); -} - diff --git a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/seq2regtable b/aphylogeo/bin/mafft-linux64/mafftdir/libexec/seq2regtable deleted file mode 100755 index 63c1bbb7..00000000 Binary files a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/seq2regtable and /dev/null differ diff --git a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/setcore b/aphylogeo/bin/mafft-linux64/mafftdir/libexec/setcore deleted file mode 100755 index 972d9fc4..00000000 Binary files a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/setcore and /dev/null differ diff --git a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/setdirection b/aphylogeo/bin/mafft-linux64/mafftdir/libexec/setdirection deleted file mode 100755 index 7651875c..00000000 Binary files a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/setdirection and /dev/null differ diff --git a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/sextet5 b/aphylogeo/bin/mafft-linux64/mafftdir/libexec/sextet5 deleted file mode 100755 index 0317b4ed..00000000 Binary files a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/sextet5 and /dev/null differ diff --git a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/splittbfast b/aphylogeo/bin/mafft-linux64/mafftdir/libexec/splittbfast deleted file mode 100755 index 741cd15d..00000000 Binary files a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/splittbfast and /dev/null differ diff --git a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/tbfast b/aphylogeo/bin/mafft-linux64/mafftdir/libexec/tbfast deleted file mode 100755 index 719f5f3c..00000000 Binary files a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/tbfast and /dev/null differ diff --git a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/version b/aphylogeo/bin/mafft-linux64/mafftdir/libexec/version deleted file mode 100755 index 00ddc594..00000000 Binary files a/aphylogeo/bin/mafft-linux64/mafftdir/libexec/version and /dev/null differ diff --git a/aphylogeo/bin/mafft-win/mafft-signed.ps1 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b/aphylogeo/bin/mafft-win/mafft.bat deleted file mode 100644 index 89a329b0..00000000 --- a/aphylogeo/bin/mafft-win/mafft.bat +++ /dev/null @@ -1,33 +0,0 @@ -@echo off -setlocal enabledelayedexpansion -cls; 1>&2 -chcp 65001 1>&2 -for /f "usebackq tokens=*" %%i IN (`cd`) DO @set current_dir=%%i -if /i "%current_dir%" == "%systemroot%" ( - set mafft_working_dir="%~dp0" -) else ( - set mafft_working_dir="%current_dir%" -) -pushd "%mafft_working_dir%" - -echo; 1>&2 -echo Preparing environment to run MAFFT on Windows. 1>&2 -echo This may take a while, if real-time scanning by anti-virus software is on. 1>&2 - -set ROOTDIR=%~d0%~p0 -set PATH=/usr/bin/:%PATH% -set MAFFT_BINARIES=/usr/lib/mafft -set TMPDIR=%TMP% -set MAFFT_TMPDIR=%TMPDIR% - -REM set TMPDIR=%ROOTDIR%/tmp -REM set MAFFT_TMPDIR=%TMPDIR% -REM If you do not have write permission for Windows temporary folder -REM (typically C:\Users\username\AppData\Local\Temp\), then -REM uncomment (remove REM) the above two lines to use an alternative -REM temporary folder. - -"%ROOTDIR%\usr\bin\bash" "/usr/bin/mafft" %* - -popd -exit /b diff --git a/aphylogeo/bin/mafft-win/testdata.txt b/aphylogeo/bin/mafft-win/testdata.txt deleted file mode 100644 index bbba8ae0..00000000 --- a/aphylogeo/bin/mafft-win/testdata.txt +++ /dev/null @@ -1,4 +0,0 @@ ->1 -acdefghijklm ->2 -ghijkm diff --git a/aphylogeo/bin/mafft-win/usr/bin/awk.exe b/aphylogeo/bin/mafft-win/usr/bin/awk.exe deleted file mode 100644 index ba7929a7..00000000 Binary files a/aphylogeo/bin/mafft-win/usr/bin/awk.exe and /dev/null differ diff --git a/aphylogeo/bin/mafft-win/usr/bin/basename.exe b/aphylogeo/bin/mafft-win/usr/bin/basename.exe deleted file mode 100644 index 3e63ef79..00000000 Binary files a/aphylogeo/bin/mafft-win/usr/bin/basename.exe and /dev/null differ diff --git a/aphylogeo/bin/mafft-win/usr/bin/bash.exe b/aphylogeo/bin/mafft-win/usr/bin/bash.exe deleted file mode 100644 index 32149dab..00000000 Binary files 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a/aphylogeo/bin/mafft-win/usr/bin/mafft +++ /dev/null @@ -1,3063 +0,0 @@ -#! /bin/bash -er=0; -myself=`dirname "$0"`/`basename "$0"`; export myself -version="v7.520 (2023/Mar/22)"; export version -LANG=C; export LANG -os=`uname` -progname=`basename "$0"` -windows="no" -if [ `echo $os | grep -i cygwin` ]; then - os="cygwin" - windows="yes" -elif [ `echo $os | grep -i msys` ]; then - os="msys" - windows="yes" -elif [ `echo $os | grep -i mingw` ]; then - os="mingw" - windows="yes" -elif [ `echo $os | grep -i darwin` ]; then - os="darwin" -elif [ `echo $os | grep -i sunos` ]; then - os="sunos" -elif [ `echo $os | grep -i linux` ]; then - os="linux" -else - os="unix" -fi -#export os # iranai -if [ "$windows" = "yes" ]; then - echo "" 1>&2 - echo "It may take a while before the calculation starts" 1>&2 - echo "if being scanned by anti-virus software." 1>&2 - echo "Also consider using a faster version for Windows 10:" 1>&2 - echo "https://mafft.cbrc.jp/alignment/software/wsl.html" 1>&2 -fi - -if [ "$MAFFT_BINARIES" ]; then - prefix="$MAFFT_BINARIES" -else - prefix=/usr/local/libexec/mafft -fi -export prefix # iranai - -if [ $# -gt 0 ]; then - if [ "$1" = "--man" ]; then - man "$prefix/mafft.1" - exit 0; - fi -fi - -if [ -x "$prefix/version" ]; then -# versionbin=`"$prefix/version" | awk '{print $1}'` # for cygwin - versionbin=`"$prefix/version"` # for cygwin 2.7 - else - versionbin="0.000" -fi - -if ! expr "$version" : v"$versionbin" > /dev/null ; then - echo "" 1>&2 - echo "v$versionbin != $version" 1>&2 - echo "" 1>&2 - echo "There is a problem in the configuration of your shell." 1>&2 - echo "Check the MAFFT_BINARIES environmental variable by" 1>&2 - echo "$ echo \$MAFFT_BINARIES" 1>&2 - echo "" 1>&2 - echo "This variable must be *unset*, unless you have installed MAFFT" 1>&2 - echo "with a special configuration. To unset this variable, type" 1>&2 - echo "$ unset MAFFT_BINARIES" 1>&2 - echo "or" 1>&2 - echo "% unsetenv MAFFT_BINARIES" 1>&2 - echo "Then retry" 1>&2 - echo "$ mafft input > output" 1>&2 - echo "" 1>&2 - echo "To keep this change permanently, edit setting files" 1>&2 - echo "(.bash_profile, .profile, .cshrc, etc) in your home directory" 1>&2 - echo "to delete the MAFFT_BINARIES line." 1>&2 - echo "On MacOSX, also edit or remove the .MacOSX/environment.plist file" 1>&2 - echo "and then re-login (MacOSX 10.6) or reboot (MacOSX 10.7)." 1>&2 - echo "" 1>&2 - echo "Please send a problem report to katoh@ifrec.osaka-u.ac.jp," 1>&2 - echo "if this problem remains." 1>&2 - echo "" 1>&2 - exit 1 - er=1 -fi - -defaultiterate=0 -defaultcycle=2 -defaultgop="1.53" -#defaultaof="0.123" -defaultaof="0.000" -defaultlaof="0.100" -defaultlgop="-2.00" -defaultfft=1 -defaultrough=0 -defaultdistance="ktuples" -#defaultdistance="local" -defaultweighti="2.7" -defaultweightr="0.0" -defaultweightm="1.0" -defaultdafs=0 -defaultmccaskill=0 -defaultcontrafold=0 -defaultalgopt=" " -defaultalgoptit=" " -defaultsbstmodel=" -b 62 " -defaultfmodel=" " -defaultkappa=" " -if [ $progname = "xinsi" -o $progname = "mafft-xinsi" ]; then - defaultfft=1 - defaultcycle=1 - defaultiterate=1000 - defaultdistance="scarna" - defaultweighti="3.2" - defaultweightr="8.0" - defaultweightm="2.0" - defaultmccaskill=1 - defaultcontrafold=0 - defaultdafs=0 - defaultalgopt=" -A " - defaultalgoptit=" -AB " ## chui - defaultaof="0.0" - defaultsbstmodel=" -b 62 " - defaultkappa=" " - defaultfmodel=" " # 2013/06/18 -elif [ $progname = "qinsi" -o $progname = "mafft-qinsi" ]; then - defaultfft=1 - defaultcycle=1 - defaultiterate=1000 - defaultdistance="global" - defaultweighti="3.2" - defaultweightr="8.0" - defaultweightm="2.0" - defaultmccaskill=1 - defaultcontrafold=0 - defaultdafs=0 - defaultalgopt=" -A " - defaultalgoptit=" -AB " ## chui - defaultaof="0.0" - defaultsbstmodel=" -b 62 " - defaultkappa=" " - defaultfmodel=" " # 2013/06/18 -elif [ $progname = "linsi" -o $progname = "mafft-linsi" ]; then - defaultfft=0 - defaultcycle=1 - defaultiterate=1000 - defaultdistance="local" -elif [ $progname = "ginsi" -o $progname = "mafft-ginsi" ]; then - defaultfft=1 - defaultcycle=1 - defaultiterate=1000 - defaultdistance="global" -elif [ $progname = "einsi" -o $progname = "mafft-einsi" ]; then - defaultfft=0 - defaultcycle=1 - defaultiterate=1000 - defaultdistance="localgenaf" -elif [ $progname = "fftns" -o $progname = "mafft-fftns" ]; then - defaultfft=1 - defaultcycle=2 - defaultdistance="ktuples" -elif [ $progname = "fftnsi" -o $progname = "mafft-fftnsi" ]; then - defaultfft=1 - defaultcycle=2 - defaultiterate=2 - defaultdistance="ktuples" -elif [ $progname = "nwns" -o $progname = "mafft-nwns" ]; then - defaultfft=0 - defaultcycle=2 - defaultdistance="ktuples" -elif [ $progname = "nwnsi" -o $progname = "mafft-nwnsi" ]; then - defaultfft=0 - defaultcycle=2 - defaultiterate=2 - defaultdistance="ktuples" -fi -outputfile="" -namelength=-1 -linelength=60 # Will change to -1 in the future -anysymbol=0 -parallelizationstrategy="BAATARI2" -kappa=$defaultkappa -sbstmodel=$defaultsbstmodel -fmodel=$defaultfmodel -nmodel=" " -gexp=0 -gop=$defaultgop -gopdist=$defaultgop -aof=$defaultaof -cycle=$defaultcycle -iterate=$defaultiterate -fft=$defaultfft -rough=$defaultrough -distance=$defaultdistance -forcefft=0 -memopt=" " -weightopt=" " -GGOP="-6.00" -LGOP="-6.00" -LEXP="-0.000" -GEXP="-0.000" -lgop=$defaultlgop -lexp="-0.100" -laof=$defaultlaof -pggop="-2.00" -pgexp="-0.10" -pgaof="0.10" -rgop="-1.530" -rgep="-0.000" -seqtype=" " -weighti=$defaultweighti -weightr=$defaultweightr -weightm=$defaultweightm -rnaalifold=0 -dafs=$defaultdafs -mccaskill=$defaultmccaskill -contrafold=$defaultcontrafold -progressfile="/dev/stderr" -anchorfile="/dev/null" -anchoropt="" -#maxanchorseparation=1000 -maxanchorseparation=-1 # 2023/Jan/11 -debug=0 -sw=0 -algopt=$defaultalgopt -algoptit=$defaultalgoptit -#algspecified=0 -pairspecified=0 -scorecalcopt=" " -coreout=0 -corethr="0.5" -corewin="100" -coreext=" " -outputformat="pir" -f2clext="-N" -outorder="input" -seed="x" -seedtable="x" -auto=0 -groupsize=-1 -partsize=50 -partdist="ktuples" -partorderopt=" -x " -treeout=0 -nodeout=0 -distout=0 -treein=0 -topin=0 -treeinopt=" " -seedfiles="/dev/null" -seedtablefile="/dev/null" -pdblist="/dev/null" -ownlist="/dev/null" -strdir="$PWD" -scorematrix="/dev/null" -textmatrix="/dev/null" -treeinfile="/dev/null" -codonposfile="/dev/null" -codonscorefile="/dev/null" -rnascoremtx=" " -laraparams="/dev/null" -foldalignopt=" " -treealg=" -X 0.1 " -sueff="1.0" -maxambiguous="1.0" -dofilter=0 -scoreoutarg=" " -numthreads=0 -numthreadsit=-1 -numthreadstb=-1 -randomseed=0 -addfile="/dev/null" -addarg0=" " -addarg=" " -addsinglearg=" " -add2ndhalfarg=" " -mapoutfile="/dev/null" -fragment=0 -legacygapopt=" " -mergetable="/dev/null" -mergearg=" " -seedoffset=0 -outnum=" " -last_e=5000 -last_m=3 -last_subopt=" " -last_once=" " -adjustdirection=0 -tuplesize=6 -termgapopt=" -O " -#termgapopt=" " # gap/gap ga kakenai node -similarityoffset="0.0" -unalignlevel="0.0" -unalignspecified=0 -spfactor="100.0" -shiftpenaltyspecified=0 -opdistspecified=0 -allowshift=0 -enrich=0 # ato de kezuru -enrichseq=0 # ato de kezuru -enrichstr=0 # ato de kezuru -seektarget="" # ato de kezuru -dashserver="https://sysimm.org/dash/REST1.0/" -newdash=0 -newdash_originalsequenceonly=0 -exclude_ho=0 -fixthreshold="0.0" -bunkatsuopt=" " -npickup=0 -minimumweight="0.00001" # 2016/Mar -usenaivepairscore=" " -oldgenafparam=0 -sprigorous=0 -treeext="none" -initialramusage="20GB" -focusarg=" " -lhlimit=" " -mpiscript="/dev/null" -if [ $# -gt 0 ]; then - if [ "$1" = "--version" ]; then - echo "$version" 1>&2 - exit 0; - elif [ "$1" = "--help" -o "$1" = "--info" ]; then - shift - er=1; - fi - while [ $# -gt 1 ]; - do - if [ "$1" = "--auto" ]; then - auto=1 - elif [ "$1" = "--anysymbol" ]; then - anysymbol=1 - elif [ "$1" = "--preservecase" ]; then - anysymbol=1 - elif [ "$1" = "--clustalout" ]; then - outputformat="clustal" - elif [ "$1" = "--phylipout" ]; then - outputformat="phylip" - elif [ "$1" = "--reorder" ]; then - outorder="aligned" - partorderopt=" " - elif [ "$1" = "--inputorder" ]; then - outorder="input" - partorderopt=" -x " - elif [ "$1" = "--unweight" ]; then - weightopt=" -u " - elif [ "$1" = "--termgappenalty" ]; then - termgapopt=" " - elif [ "$1" = "--alga" ]; then - algopt=" " - algoptit=" " -# algspecified=1 - elif [ "$1" = "--algq" ]; then - algopt=" -Q " - algoptit=" " - echo "" 1>&2 - echo "--algq is no longer supported!" 1>&2 - echo "" 1>&2 - exit 1; -# algspecified=1 - elif [ "$1" = "--linelength" ]; then - shift - linelength=`expr "$1" - 0` - if [ $linelength -eq 0 ]; then - echo "Line length = 0 ?" 1>&2 - exit - fi - elif [ "$1" = "--namelength" ]; then - shift - namelength=`expr "$1" - 0` - if ! expr "$1" : "[0-9]" > /dev/null ; then - echo "Specify the length of name in clustal format output!" 1>&2 - exit - fi - elif [ "$1" = "--groupsize" ]; then - shift - groupsize=`expr "$1" - 0` - if ! expr "$1" : "[0-9]" > /dev/null ; then - echo "Specify groupsize!" 1>&2 - exit - fi - elif [ "$1" = "--partsize" ]; then - shift - partsize=`expr "$1" - 0` - if ! expr "$1" : "[0-9]" > /dev/null ; then - echo "Specify partsize!" 1>&2 - exit - fi - elif [ "$1" = "--parttree" ]; then - distance="parttree" - partdist="ktuples" - elif [ "$1" = "--dpparttree" ]; then - distance="parttree" - partdist="localalign" - elif [ "$1" = "--fastaparttree" ]; then - distance="parttree" - partdist="fasta" - elif [ "$1" = "--treeout" ]; then - treeout=1 - elif [ "$1" = "--nodeout" ]; then - nodeout=1 - treeout=1 - elif [ "$1" = "--distout" ]; then - distout=1 - elif [ "$1" = "--fastswpair" ]; then - distance="fasta" - pairspecified=1 - sw=1 - elif [ "$1" = "--fastapair" ]; then - distance="fasta" - pairspecified=1 - sw=0 - elif [ "$1" = "--averagelinkage" ]; then - treealg=" -X 1.0 " - sueff="1.0" - elif [ "$1" = "--minimumlinkage" ]; then - treealg=" -X 0.0 " - sueff="0.0" - elif [ "$1" = "--mixedlinkage" ]; then - shift - sueff="$1" - treealg=" -X $1" - elif [ "$1" = "--maxambiguous" ]; then - shift - maxambiguous="$1" - dofilter=1 - elif [ "$1" = "--codonpos" ]; then - shift - codonposfile="$1" - if [ ! -e "$codonposfile" ]; then - echo "Cannot open $codonposfile" 1>&2 - echo "" 1>&2 - exit - fi - codonposopt=" -R " - elif [ "$1" = "--codonscore" ]; then - shift - codonscorefile="$1" - if [ ! -e "$codonscorefile" ]; then - echo "Cannot open $codonscorefile" 1>&2 - echo "" 1>&2 - exit - fi - codonscoreopt=" -S " - elif [ "$1" = "--noscore" ]; then - scorecalcopt=" -Z " - elif [ "$1" = "--6mermultipair" ]; then - distance="ktuplesmulti" - tuplesize=6 - pairspecified=1 - elif [ "$1" = "--10mermultipair" ]; then - distance="ktuplesmulti" - tuplesize=10 - pairspecified=1 - elif [ "$1" = "--6merpair" ]; then - distance="ktuples" - tuplesize=6 - pairspecified=1 - elif [ "$1" = "--10merpair" ]; then - distance="ktuples" - tuplesize=10 - pairspecified=1 - elif [ "$1" = "--blastpair" ]; then - distance="blast" - pairspecified=1 - elif [ "$1" = "--lastmultipair" ]; then - distance="lastmulti" - pairspecified=1 - elif [ "$1" = "--globalpair" ]; then - distance="global" - pairspecified=1 - elif [ "$1" = "--shortlongpair" ]; then - distance="local" - usenaivepairscore="-Z" - laof=0.0 # addfull no tokini tsukawareru. - lexp=0.0 # addfull no tokini tsukawareru. - pgaof=0.0 # local nara iranai - pgexp=0.0 # local nara iranai - pairspecified=1 - elif [ "$1" = "--longshortpair" ]; then - distance="local" - usenaivepairscore="-Z" - laof=0.0 # addfull no tokini tsukawareru. - lexp=0.0 # addfull no tokini tsukawareru. - pgaof=0.0 # local nara iranai - pgexp=0.0 # local nara iranai - pairspecified=1 - elif [ "$1" = "--localpair" ]; then - distance="local" - pairspecified=1 - elif [ "$1" = "--lastpair" ]; then - distance="last" - pairspecified=1 - elif [ "$1" = "--multipair" ]; then - distance="multi" - pairspecified=1 - elif [ "$1" = "--hybridpair" ]; then - distance="hybrid" - pairspecified=1 - elif [ "$1" = "--scarnapair" ]; then - distance="scarna" - pairspecified=1 - elif [ "$1" = "--dafspair" ]; then - distance="dafs" - pairspecified=1 - elif [ "$1" = "--larapair" ]; then - distance="lara" - pairspecified=1 - elif [ "$1" = "--slarapair" ]; then - distance="slara" - pairspecified=1 - elif [ "$1" = "--foldalignpair" ]; then - distance="foldalignlocal" - pairspecified=1 - elif [ "$1" = "--foldalignlocalpair" ]; then - distance="foldalignlocal" - pairspecified=1 - elif [ "$1" = "--foldalignglobalpair" ]; then - distance="foldalignglobal" - pairspecified=1 - elif [ "$1" = "--globalgenafpair" ]; then - distance="globalgenaf" - pairspecified=1 - echo "" 1>&2 - echo "--globalgenaf is no longer supported!" 1>&2 - echo "" 1>&2 - exit 1; - elif [ "$1" = "--localgenafpair" ]; then - distance="localgenaf" - pairspecified=1 - elif [ "$1" = "--genafpair" ]; then - distance="localgenaf" - pairspecified=1 - elif [ "$1" = "--oldgenafpair" ]; then - distance="localgenaf" - pairspecified=1 - oldgenafparam=1 - elif [ "$1" = "--memsave" ]; then - memopt=" -M -B " # -B (bunkatsunashi no riyu ga omoidasenai) - elif [ "$1" = "--nomemsave" ]; then - memopt=" -N " - elif [ "$1" = "--nuc" ]; then - seqtype="-D" # Deleted space, 2018/Dec - elif [ "$1" = "--amino" ]; then - seqtype="-P" # Deleted space, 2018/Dec - elif [ "$1" = "--fft" ]; then - fft=1 - forcefft=1 - elif [ "$1" = "--nofft" ]; then - fft=0 - elif [ "$1" = "--quiet" ]; then -# if [ $os = "msys" ]; then -# progressfile="nul" -# else - progressfile="/dev/null" -# fi - elif [ "$1" = "--debug" ]; then - debug=1 - elif [ "$1" = "--coreext" ]; then - coreext=" -c " - elif [ "$1" = "--core" ]; then - coreout=1 - elif [ "$1" = "--adjustdirection" ]; then - adjustdirection=1 - elif [ "$1" = "--adjustdirectionaccurately" ]; then - adjustdirection=2 - elif [ "$1" = "--oneiteration" ]; then - oneiterationopt=" -r " - elif [ "$1" = "--progress" ]; then - shift - progressfile="$1" - if ! ( expr "$progressfile" : "\/" > /dev/null || expr "$progressfile" : "[A-Za-z]\:" > /dev/null ) ; then - echo "Specify a progress file name with the absolute path!" 1>&2 - exit - fi - elif [ "$1" = "--out" ]; then - shift - outputfile="$1" - elif [ "$1" = "--skipanchorsremoterthan" ]; then - shift - if ! expr "$1" : "[0-9]" > /dev/null ; then - echo "Specify maximum gap length between anchors." 1>&2 - exit - fi - maxanchorseparation=`expr "$1" - 0` - elif [ "$1" = "--anchors" ]; then - shift - anchorfile="$1" - anchoropt=" -l " -# memopt=" -M -B " # ato de kentou -# memopt=" -N " # no memsave - if [ ! -e "$anchorfile" ]; then - echo "Cannot open $anchorfile" 1>&2 - echo "" 1>&2 - exit - fi - elif [ "$1" = "--thread" ]; then - shift - if ! expr "$1" : "[0-9\-]" > /dev/null ; then - echo "Specify the number of threads. Or, use --thread -1" 1>&2 - exit - fi - numthreads=`expr "$1" - 0` - elif [ "$1" = "--threadtb" ]; then - shift - if ! expr "$1" : "[0-9\-]" > /dev/null ; then - echo "Check the argument after --threadtb, the number of threads for the progressive step." 1>&2 - exit - fi - numthreadstb=`expr "$1" - 0` - elif [ "$1" = "--threadit" ]; then - shift - if ! expr "$1" : "[0-9\-]" > /dev/null ; then - echo "Check the argument after --threadit, the number of threads for the iterative step." 1>&2 - exit - fi - numthreadsit=`expr "$1" - 0` - elif [ "$1" = "--last_subopt" ]; then - last_subopt="-S" - elif [ "$1" = "--last_once" ]; then - last_once="-U" - elif [ "$1" = "--last_m" ]; then - shift - last_m=`expr "$1" - 0` - elif [ "$1" = "--last_e" ]; then - shift - last_e=`expr "$1" - 0` - elif [ "$1" = "--randomseed" ]; then - shift - randomseed=`expr "$1" - 0` - elif [ "$1" = "--bestfirst" ]; then - parallelizationstrategy="BESTFIRST" - elif [ "$1" = "--adhoc0" ]; then - parallelizationstrategy="BAATARI0" - elif [ "$1" = "--adhoc1" ]; then - parallelizationstrategy="BAATARI1" - elif [ "$1" = "--adhoc2" ]; then - parallelizationstrategy="BAATARI2" - elif [ "$1" = "--simplehillclimbing" ]; then - parallelizationstrategy="BAATARI2" - elif [ "$1" = "--scoreout" ]; then - scoreoutarg="-S -B" - elif [ "$1" = "--outnum" ]; then - outnum="-n" - elif [ "$1" = "--leavegappyregion" ]; then - legacygapopt="-L" - elif [ "$1" = "--legacygappenalty" ]; then - legacygapopt="-L" - elif [ "$1" = "--merge" ]; then - shift - mergetable="$1" - if [ ! -e "$mergetable" ]; then - echo "Cannot open $mergetable" 1>&2 - echo "" 1>&2 - exit - fi - elif [ "$1" = "--addprofile" ]; then - shift - addarg0="-I" - addfile="$1" - elif [ "$1" = "--add" ]; then - shift - addarg0="-K -I" - addfile="$1" - elif [ "$1" = "--addfragments" ]; then - shift - addarg0="-K -I" - addfile="$1" - fragment=1 - elif [ "$1" = "--addfull" ]; then - shift - addarg0="-K -I" - addfile="$1" - fragment=-1 - elif [ "$1" = "--addlong" ]; then - shift - addarg0="-K -I" - addfile="$1" - fragment=-2 - elif [ "$1" = "--addtotop" ]; then - shift - addarg0="-K -I" - addfile="$1" - fragment=-3 - elif [ "$1" = "--addtoroot" ]; then - shift - addarg0="-K -I" - addfile="$1" - fragment=-4 - elif [ "$1" = "--smoothing" ]; then - add2ndhalfarg=$add2ndhalfarg" -p " - elif [ "$1" = "--keeplength" ]; then - add2ndhalfarg=$add2ndhalfarg" -Y " - elif [ "$1" = "--compactmapout" ]; then - add2ndhalfarg=$add2ndhalfarg" -z -Y " - elif [ "$1" = "--compactmapoutfile" ]; then - shift - add2ndhalfarg=$add2ndhalfarg" -z -Y " - mapoutfile="$1" - elif [ "$1" = "--mapout" ]; then - add2ndhalfarg=$add2ndhalfarg" -Z -Y " - elif [ "$1" = "--mapoutfile" ]; then - shift - add2ndhalfarg=$add2ndhalfarg" -Z -Y " - mapoutfile="$1" - elif [ "$1" = "--maxiterate" ]; then - shift - iterate=`expr "$1" - 0` - if ! expr "$1" : "[0-9]" > /dev/null ; then - echo "Specify the number of iterations!" 1>&2 - exit - fi - elif [ "$1" = "--retree" ]; then - shift - cycle=`expr "$1" - 0` - if ! expr "$1" : "[0-9]" > /dev/null ; then - echo "Specify the number of tree rebuilding!" 1>&2 - exit - fi - elif [ "$1" = "--aamatrix" ]; then - shift - f2clext="-N" - sbstmodel=" -b -1 " - scorematrix="$1" - if [ ! -e "$scorematrix" ]; then - echo "Cannot open $scorematrix" 1>&2 - echo "" 1>&2 - exit - fi - elif [ "$1" = "--textmatrix" ]; then - shift - f2clext="-E" - seqtype="-P" - fft=0 -# sbstmodel=" -b -2 -a " - sbstmodel=" -b -2 " # 2022/Jul, hauretsu no kawari ni scoremtx wo miru - scorematrix="$1" - if [ ! -e "$scorematrix" ]; then - echo "Cannot open $scorematrix" 1>&2 - echo "" 1>&2 - exit - fi - elif [ "$1" = "--text" ]; then - f2clext="-E" - seqtype="-P" - fft=0 - sbstmodel=" -b -2 -a " - elif [ "$1" = "--treein" ]; then - shift - treeinopt=" -U " - treein=1 - treeinfile="$1" - if [ ! -e "$treeinfile" ]; then - echo "Cannot open $treeinfile" 1>&2 - echo "" 1>&2 - exit - fi - elif [ "$1" = "--pileup" ]; then -# treeinopt=" -U " -# treein=1 - treeext="pileup" - elif [ "$1" = "--randomchain" ]; then -# treeinopt=" -U " -# treein=1 -# pileuporshuffle="s" - treeext="randomchain" - elif [ "$1" = "--topin" ]; then - shift - treeinopt=" -V " - treein=1 - treeinfile="$1" - echo "The --topin option has been disabled." 1>&2 - echo "There was a bug in version < 6.530." 1>&2 - echo "This bug has not yet been fixed." 1>&2 - exit 1 - elif [ "$1" = "--mpi" ]; then - mpiscript="$prefix/mpiscript" - elif [ "$1" = "--large" ]; then - treeext="memsavetree" - elif [ "$1" = "--memsavetree" ]; then - treeext="memsavetree" - elif [ "$1" = "--memsavetreex" ]; then - treeext="memsavetreex" - elif [ "$1" = "--stepadd" ]; then - treeext="stepadd" - elif [ "$1" = "--youngestlinkage" ]; then - treeext="youngestlinkage" - elif [ "$1" = "--kappa" ]; then - shift - kappa=" -k $1 " - if ! expr "$1" : "[0-9]" > /dev/null ; then - echo "Specify kappa value!" 1>&2 - exit - fi - elif [ "$1" = "--fmodel" ]; then - fmodel=" -a " - elif [ "$1" = "--nwildcard" ]; then - nmodel=" -: " - elif [ "$1" = "--nzero" ]; then - nmodel=" " - elif [ "$1" = "--jtt" ]; then - shift - f2clext="-N" - sbstmodel=" -j $1" -# if ! expr "$1" : "[0-9]" > /dev/null ; then -# echo "Specify pam value!" 1>&2 -# exit -# fi - elif [ "$1" = "--kimura" ]; then - shift - f2clext="-N" - sbstmodel=" -j $1" -# if ! expr "$1" : "[0-9]" > /dev/null ; then -# echo "Specify pam value!" 1>&2 -# exit -# fi - elif [ "$1" = "--tm" ]; then - shift - f2clext="-N" - sbstmodel=" -m $1" -# if ! expr "$1" : "[0-9]" > /dev/null ; then -# echo "Specify pam value!" 1>&2 -# exit -# fi - elif [ "$1" = "--bl" ]; then - shift - f2clext="-N" - sbstmodel=" -b $1" - if ! expr "$1" : "[0-9]" > /dev/null ; then - echo "blosum $1?" 1>&2 - exit - fi - elif [ "$1" = "--weighti" ]; then - shift - weighti="$1" - if ! expr "$1" : "[0-9]" > /dev/null ; then - echo "Specify weighti value!" 1>&2 - exit - fi - elif [ "$1" = "--weightr" ]; then - shift - weightr="$1" - if ! expr "$1" : "[0-9]" > /dev/null ; then - echo "Specify weightr value!" 1>&2 - exit - fi - elif [ "$1" = "--weightm" ]; then - shift - weightm="$1" - if ! expr "$1" : "[0-9]" > /dev/null ; then - echo "Specify weightm value!" 1>&2 - exit - fi - elif [ "$1" = "--rnaalifold" ]; then - rnaalifold=1 - elif [ "$1" = "--mccaskill" ]; then - mccaskill=1 - contrafold=0 - dafs=0 - elif [ "$1" = "--contrafold" ]; then - mccaskill=0 - contrafold=1 - dafs=0 - elif [ "$1" = "--dafs" ]; then - mccaskill=0 - contrafold=0 - dafs=1 - elif [ "$1" = "--ribosum" ]; then - rnascoremtx=" -s " - elif [ "$1" = "--op" ]; then - shift - gop="$1" - if ! expr "$1" : "[0-9]" > /dev/null ; then - echo "Specify op!" 1>&2 - exit - fi - elif [ "$1" = "--opdist" ]; then - shift - gopdist="$1" - if ! expr "$1" : "[0-9]" > /dev/null ; then - echo "Specify opdist!" 1>&2 - exit - fi - opdistspecified=1 - elif [ "$1" = "--allowshift" ]; then - allowshift=1 - elif [ "$1" = "--shiftpenalty" ]; then - shift - spfactor="$1" - if ! expr "$1" : "[0-9]" > /dev/null ; then - echo "Specify sf!" 1>&2 - exit - fi - shiftpenaltyspecified=1 - elif [ "$1" = "--exp" ]; then - shift -# gexp="$1" - tmpval="$1" - gexp=`awk "BEGIN{ print -1.0 * \"$tmpval\"}"` - if ! expr "$gexp" : "[0-9\-]" > /dev/null ; then - printf "\nSpecify a number for exp, like --exp 0.1\n" 1>&2 - printf "'$1' cannot be interpreted as a number..\n\n" 1>&2 - exit - fi - elif [ "$1" = "--ep" ]; then - shift -# aof="$1" - tmpval="$1" - aof=`awk "BEGIN{ print -1.0 * \"$tmpval\"}"` - if ! expr "$aof" : "[0-9\-]" > /dev/null ; then - printf "\nSpecify a number for ep, like --ep 0.1\n" 1>&2 - printf "'$1' cannot be interpreted as a number..\n\n" 1>&2 - exit - fi - elif [ "$1" = "--rop" ]; then - shift - rgop="$1" -# Atode check - elif [ "$1" = "--rep" ]; then - shift - rgep="$1" - elif [ "$1" = "--lop" ]; then - shift - lgop="$1" - elif [ "$1" = "--LOP" ]; then - shift - LGOP="$1" - elif [ "$1" = "--lep" ]; then - shift - laof="$1" - elif [ "$1" = "--lexp" ]; then - shift - lexp="$1" - elif [ "$1" = "--LEXP" ]; then - shift - LEXP="$1" - elif [ "$1" = "--GEXP" ]; then - shift - GEXP="$1" - elif [ "$1" = "--GOP" ]; then - shift - GGOP="$1" - elif [ "$1" = "--gop" ]; then - shift - pggop="$1" - elif [ "$1" = "--gep" ]; then - shift - pgaof="$1" - elif [ "$1" = "--gexp" ]; then - shift - pgexp="$1" - elif [ "$1" = "--laraparams" ]; then - shift - laraparams="$1" - elif [ "$1" = "--corethr" ]; then - shift - corethr="$1" - elif [ "$1" = "--corewin" ]; then - shift - corewin="$1" - elif [ "$1" = "--strdir" ]; then - shift - strdir="$1" - elif [ "$1" = "--pdbidlist" ]; then - echo "--pdbidlist is temporarily unavailable, 2018/Dec." 1>&2 - echo "" 1>&2 - exit - shift - pdblist="$1" - if [ ! -e "$pdblist" ]; then - echo "Cannot open $pdblist" 1>&2 - echo "" 1>&2 - exit - fi - elif [ "$1" = "--pdbfilelist" ]; then - echo "--pdbfilelist is temporarily unavailable, 2018/Dec." 1>&2 - echo "" 1>&2 - exit - shift - ownlist="$1" - if [ ! -e "$ownlist" ]; then - echo "Cannot open $ownlist" 1>&2 - echo "" 1>&2 - exit - fi -# elif [ "$1" = "--enrich" ]; then -# enrich=1 -# enrichseq=1 -# enrichstr=1 -# seektarget="" -# elif [ "$1" = "--enrichseq" ]; then -# enrich=1 -# enrichseq=1 -# enrichstr=0 -# seektarget="-seq" -# elif [ "$1" = "--enrichstr" ]; then -# enrich=1 -# enrichseq=0 -# enrichstr=1 -# seektarget="-str" - elif [ "$1" = "--dash" ]; then - newdash=1 - if [ "$distance" != "local" -a "$distance" != "localgenaf" ]; then # 2021/Oct - distance="global" - fi - if [ "$iterate" -eq 0 ]; then # 2021/Oct - iterate=3 - fi - elif [ "$1" = "--dashserver" ]; then - shift - dashserver="$1" - elif [ "$1" = "--originalseqonly" ]; then - newdash_originalsequenceonly=1 - elif [ "$1" = "--excludehomologs" ]; then # works with --dash only - exclude_ho=1 - elif [ "$1" = "--seedtable" ]; then - shift - seedtable="y" - seedtablefile="$1" - elif [ "$1" = "--seed" ]; then - shift - seed="m" - seedfiles="$seedfiles $1" - elif [ "$1" = "--minimumweight" ]; then - shift - minimumweight="$1" - elif [ "$1" = "--similaritylevel" ]; then - shift - similarityoffset="$1" - elif [ "$1" = "--unalignlevel" ]; then - shift - unalignlevel="$1" - unalignspecified=1 - elif [ "$1" = "--skipiterate" ]; then - shift - fixthreshold="$1" - elif [ "$1" = "--bunkatsunashi" ]; then - bunkatsuopt=" -B " - elif [ "$1" = "--sp" ]; then - sprigorous=1 - elif [ "$1" = "--focus" ]; then - focusarg=" -= " - elif [ "$1" = "--lhlimit" ]; then # atode namae henkou - shift - lhlimit=" -q $1 " - elif [ "$1" = "--sparsepickup" ]; then - shift - npickup="$1" - elif [ $progname = "fftns" -o $progname = "nwns" ]; then - if [ "$1" -gt 0 ]; then - cycle=`expr "$1" - 0` - fi - else - echo "Unknown option: $1" 1>&2 - er=1; -# exit 1; - fi - shift - done; - - -# echo "" 1>"$progressfile" - - if [ $treeext = "memsavetree" ] || [ $treeext = "stepadd" ]; then - if [ $distance != "ktuples" ]; then -# auto -> memsave && globalpair ha erabarenai node, -# ~/maffttmp wo tsukau noha meijiteki ni shitei saretatoki dake. - if [ ! "$MAFFT_TMPDIR" ]; then # space is acceptable, 2018/Mar/17 - MAFFT_TMPDIR="$HOME/maffttmp" - mkdir -p "$MAFFT_TMPDIR" || exit - fi - fi - fi - - - if [ ! "$MAFFT_TMPDIR" ]; then - MAFFT_TMPDIR="$TMPDIR" - fi - - TMPFILE=`env TMPDIR="$MAFFT_TMPDIR" mktemp -dt "$progname.XXXXXXXXXX"` - if [ $? -ne 0 ]; then - echo "mktemp seems to be obsolete. Re-trying without -t" 1>&2 - mkdir -p "$MAFFT_TMPDIR/tmp" 1>&2 - TMPFILE=`mktemp -d "$MAFFT_TMPDIR/tmp/$progname.XXXXXXXXXX"` - fi - -# lfs getstripe $TMPFILE 2>/dev/null && lfs setstripe -c 1 $TMPFILE # 2017/Oct - lfs getstripe "$TMPFILE" > /dev/null 2>&1 && lfs setstripe -c 1 "$TMPFILE" > /dev/null 2>&1 # 2018/Feb - - if [ $os = "cygwin" ]; then - TMPFILE=`cygpath -w "$TMPFILE"` # necessary to pass path to f2cl on cyswin, somehow unnecessary in msys. - fi - -# umask 077 # 2021/Jan -# mkdir "$TMPFILE" || er=1 - - -function removetmpfile() { # for MPI - while true - do - rm -rf "$TMPFILE" && break - echo Retrying to remove "$TMPFILE". It may take several seconds. 1>&2 - sleep 2 - done -} - - if [ $debug -eq 1 ]; then -# trap "tar cfvz debuginfo.tgz $TMPFILE; rm -rf $TMPFILE " 0 # does not work in msys -# trap "tar cfv - $TMPFILE | gzip -c > debuginfo.tgz; rm -rf $TMPFILE " 0 15 - trap "popd > /dev/null 2>&1; tar cfv - \"$TMPFILE\" | gzip -c > debuginfo.tgz; removetmpfile" 0 15 - else -# trap "rm -rf $TMPFILE" 0 15 - trap "removetmpfile" 0 15 - fi - if [ $# -eq 1 ]; then - if [ -r "$1" -o "$1" = - ]; then - - if [ -r "$addfile" ]; then - printf ''; - else - echo "$0": Cannot open "$addfile". 1>&2 - echo "" 1>&2 - exit 1; - fi - - - cat "$1" | tr "\r" "\n" > "$TMPFILE/infile" - echo "" >> "$TMPFILE/infile" - cat "$addfile" | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/_addfile" - - if [ $dofilter -eq 1 ]; then -# mv "$TMPFILE/infile" "$TMPFILE/_tofilter" -# "$prefix/filter" -m $maxambiguous $seqtype -i "$TMPFILE/_tofilter" > "$TMPFILE/infile" 2>>"$progressfile" || exit 1 - mv "$TMPFILE/_addfile" "$TMPFILE/_tofilter" - "$prefix/filter" -m $maxambiguous $seqtype -i "$TMPFILE/_tofilter" > "$TMPFILE/_addfile" 2>>"$progressfile" || exit 1 - fi - cat "$TMPFILE/_addfile" >> "$TMPFILE/infile" - - cat "$scorematrix" | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/_aamtx" - cat "$mergetable" | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/_subalignmentstable" - cat "$treeinfile" | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/_guidetree" - cat "$codonposfile" | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/_codonpos" - cat "$codonscorefile" | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/_codonscore" - cat "$seedtablefile" | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/_seedtablefile" - cat "$laraparams" | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/_lara.params" - cat "$pdblist" | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/pdblist" - cat "$ownlist" | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/ownlist" - cat "$anchorfile" | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/_externalanchors" - - SAVEIFS=$IFS -# Fixed a bug: 'n' was misinterpreted as delimiter, 2020/Jun/19 - IFS=$'\n' - filelist="$1 -$addfile -$scorematrix -$mergetable -$treeinfile -$codonposfile -$codonscorefile -$seedtablefile -$laraparams -$pdblist -$ownlist" - for f in $filelist; do - file "$f" 2>/dev/null | grep -e 'UTF-16' -e 'UTF-32' >& /dev/null && printf "$f: UTF-16 or UTF-32? Convert this file to ASCII\n\n" 1>&2 && exit 1; - done - IFS=$SAVEIFS - -# echo $seedfiles - infilename="$1" - seedfilesintmp="/dev/null" - seednseq="0" - set $seedfiles > /dev/null - while [ $# -gt 1 ]; - do - shift - if [ -r "$1" ]; then - cat "$1" | tr "\r" "\n" > "$TMPFILE/seed$#" - file "$1" | grep -e 'UTF-16' -e 'UTF-32' >& /dev/null && printf "$1: UTF-16 or UTF-32? Convert this file to ASCII\n\n" 1>&2 && exit 1; - else - echo "$0": Cannot open "$1". 1>&2 - echo "" 1>&2 - exit 1; - fi - seednseq=$seednseq" "`grep -c '^[>|=]' "$TMPFILE/seed$#"` - seedfilesintmp=$seedfilesintmp" "seed$# - done -# ls $TMPFILE -# echo $seedfilesintmp -# echo $seednseq - - - else - echo "$0": Cannot open "$1". 1>&2 - echo "" 1>&2 - er=1 -# exit 1; - fi - else -# echo '$#'"=$#" 1>&2 - er=1 - fi - - - if [ $numthreads -lt 0 ]; then - if [ $os = "linux" ]; then - nlogicalcore=`cat /proc/cpuinfo | grep "^processor" | uniq | wc -l` - ncoresinacpu=`cat /proc/cpuinfo | grep 'cpu cores' | uniq | awk '{print $4}'` - nphysicalcpu=`cat /proc/cpuinfo | grep 'physical id' | sort | uniq | wc -l` - if [ $nlogicalcore -eq 0 ]; then - echo "Cannot get the number of processors from /proc/cpuinfo" 1>>"$progressfile" - exit 1 - fi - if [ ${#ncoresinacpu} -gt 0 -a $nphysicalcpu -gt 0 ]; then - numthreads=`expr $ncoresinacpu '*' $nphysicalcpu` -# if [ $nlogicalcore -gt $numthreads ]; then # Hyperthreading -# numthreads=`expr $numthreads '+' 1` -# fi - else - numthreads=$nlogicalcore - fi - elif [ $os = "darwin" ]; then - numthreads=`sysctl -n hw.physicalcpu` - if [ -z $numthreads ]; then - echo "Cannot get the number of physical cores from sysctl" 1>>"$progressfile" - exit 1 - fi -# nlogicalcore=`sysctl -n hw.logicalcpu` -# if [ $nlogicalcore -gt $numthreads ]; then # Hyperthreading -# numthreads=`expr $numthreads '+' 1` -# fi - elif [ "$windows" = "yes" ]; then -# numthreads=`wmic cpu get NumberOfCores | head -2 | tail -1 | awk '{print $1}'` - numthreads=`wmic cpu get NumberOfCores | awk 'BEGIN{n=0} {n+=$1} END{print n}'` - - else - echo "Cannot count the number of physical cores." 1>>"$progressfile" - exit 1 - fi - echo "OS = "$os 1>>"$progressfile" - echo "The number of physical cores = " $numthreads 1>>"$progressfile" - fi - - if [ $numthreadstb -lt 0 ]; then - if [ $numthreads -lt 16 -o "$mpiscript" != "/dev/null" ]; then # mpi: museigen, multithread: 16 made -# if [ $numthreads -lt 31 ]; then - numthreadstb=$numthreads - else - numthreadstb=16 - fi - fi - - if [ $numthreadsit -lt 0 ]; then - if [ $numthreads -lt 8 ]; then - numthreadsit=$numthreads - else - numthreadsit=8 - fi - fi - - if [ $numthreadsit -eq 0 -a $parallelizationstrategy = "BESTFIRST" ]; then - echo 'Impossible' 1>&2; - exit 1; - fi - - - if [ "$addarg0" != " " ]; then - -# iterate=0 # 2013/03/23 -> commented out, 2017/12 - "$prefix/countlen" < "$TMPFILE/_addfile" > "$TMPFILE/addsize" 2>>"$progressfile" - nadd=`awk '{print $1}' "$TMPFILE/addsize"` - if [ $nadd -eq "0" ]; then - echo Check $addfile 1>&2 - exit 1; - fi - if [ $seed != "x" -o $seedtable != "x" ]; then - echo 'Impossible' 1>&2; - echo 'Use either ONE of --seed, --seedtable, --addprofile and --add.' 1>&2 - exit 1; - fi - else - nadd="0" - fi - - if [ $auto -eq 1 ]; then - "$prefix/countlen" < "$TMPFILE/infile" > "$TMPFILE/size" 2>>"$progressfile" - nseq=`awk '{print $1}' "$TMPFILE/size"` - nlen=`awk '{print $3}' "$TMPFILE/size"` - - if [ $nlen -lt 3000 -a $nseq -lt 100 ]; then - distance="local" - iterate=1000 - cycle=1 - treeext="none" - elif [ $nlen -lt 1000 -a $nseq -lt 200 ]; then - distance="local" - iterate=2 - cycle=1 - treeext="none" - elif [ $nlen -lt 10000 -a $nseq -lt 500 ]; then - distance="ktuples" - iterate=2 - cycle=2 - treeext="none" - elif [ $nseq -lt 20000 ]; then # changed from 10000 2014/Oct/4 - distance="ktuples" - iterate=0 - cycle=2 - treeext="none" - elif [ $nseq -lt 100000 ]; then # changed from 50000 2017/Nov/24 - distance="ktuples" - iterate=0 - cycle=2 - if [ $fragment -eq 0 -a "$mergetable" = "/dev/null" ]; then - treeext="memsavetree" - fi - elif [ $nseq -lt 200000 ]; then # changed from 90000 2017/Nov/24 - distance="ktuples" - iterate=0 - cycle=1 - if [ $fragment -eq 0 -a "$mergetable" = "/dev/null" ]; then - treeext="memsavetree" - fi - elif [ $nlen -lt 3000 ]; then - distance="parttree" - partdist="localalign" - algopt=" " - algoptit=" " -# algspecified=1 - cycle=1 - else - distance="parttree" - partdist="ktuples" - algopt=" " - algoptit=" " -# algspecified=1 - cycle=1 - fi - - -# if [ $nlen -lt 3000 -a $nseq -lt 100 ]; then -# distance="local" -# iterate=1000 -# cycle=1 -# elif [ $nlen -lt 1000 -a $nseq -lt 200 ]; then -# distance="local" -# iterate=2 -# cycle=1 -# elif [ $nlen -lt 10000 -a $nseq -lt 500 ]; then -# distance="ktuples" -# iterate=2 -# cycle=2 -# elif [ $nseq -lt 200000 ]; then -# distance="ktuples" -# iterate=0 -# treeinopt=" -U " -# treein=1 -# pileuporshuffle="a" -# elif [ $nlen -lt 3000 ]; then -# distance="parttree" -# partdist="localalign" -# algopt=" " -# algoptit=" " -## algspecified=1 -# cycle=1 -# else -# distance="parttree" -# partdist="ktuples" -# algopt=" " -# algoptit=" " -## algspecified=1 -# cycle=1 -# fi - - - if [ $fragment -ne 0 ]; then - norg=`expr $nseq '-' $nadd` - npair=`expr $norg '*' $nadd` - echo "nadd = " $nadd 1>>"$progressfile" - echo "npair = " $npair 1>>"$progressfile" - echo "nseq = " $nseq 1>>"$progressfile" - echo "nlen = " $nlen 1>>"$progressfile" - - if [ $norg -eq 0 ]; then - echo "" 1>>"$progressfile" - echo "The reference sequence was removed because of ambiguous letters?" 1>>"$progressfile" - echo "" 1>>"$progressfile" - exit 1; - fi -# nagasa check! -# if [ $npair -gt 10000000 -o $nlen -gt 5000 ]; then # 2017/Oct - if [ $npair -gt 10000000 -o $nlen -gt 5000 -o $nadd -gt 500000 ]; then # 2021/Dec pairlocalalign to buntan - distance="ktuples" - echo "use ktuples, size=$tuplesize!" 1>>"$progressfile" -# elif [ $npair -gt 3000000 -o $nlen -gt 5000 ]; then # 2017/Oct - elif [ $npair -gt 3000000 -o $nlen -gt 5000 ]; then # 2017/Oct - distance="multi" - weighti="0.0" - echo "use multipair, weighti=0.0!" 1>>"$progressfile" - else - distance="multi" - echo "use multipair, weighti=$weighti!" 1>>"$progressfile" - fi - pairspecified=1 - fi - fi - - if [ `awk "BEGIN {print( 0.0+\"$sueff\" < 0.0 || 0.0+\"$sueff\" > 1.0 )}"` -gt 0 ]; then - printf "\n%s\n\n" "The argument of --mixedlinkage must be between 0.0 and 1.0" 1>>"$progressfile" - exit 1; - fi - - if [ `awk "BEGIN {print( 0.0+\"$maxambiguous\" < 0.0 || 0.0+\"$maxambiguous\" > 1.0 )}"` -gt 0 ]; then - printf "\n%s\n\n" "The argument of --maxambiguous must be between 0.0 and 1.0" 1>>"$progressfile" - exit 1; - fi - - if [ $allowshift -eq 1 ]; then - if [ $unalignspecified -ne 1 ]; then - unalignlevel="0.8" - fi - if [ $shiftpenaltyspecified -ne 1 ]; then - spfactor="2.00" - fi - fi - - if [ $opdistspecified -ne 1 ]; then - gopdist=$gop - fi - - if [ $unalignlevel != "0.0" -o `awk "BEGIN {print( 0.0+\"$spfactor\" < 100.0 )}"` -gt 0 ]; then - nmodel=" -: " - termgapopt=" " - if [ $distance = "localgenaf" ]; then - printf "\n%s\n" "The combination of --allowshift and --genafpair (E-INS-i/-1) is not supported." 1>>"$progressfile" - printf "%s\n" "Instead, please try --allowshift --globalpair (G-INS-i/-1 in the web version)," 1>>"$progressfile" - printf "%s\n\n" "which covers the situation for --genafpair (E-INS-i/-1), too." 1>>"$progressfile" - exit 1; - fi - if [ $distance != "global" -o `awk "BEGIN {print( 0.0+\"$weighti\" < 1.0 )}"` -gt 0 ]; then - printf "\n%s\n\n" "At present, --unalignlevel # or --allowshift is supported only with the --globalpair option." 1>>"$progressfile" - exit 1; - fi - if [ $fragment -ne 0 ]; then - printf "\n%s\n\n" "At present, --unalignlevel # or --allowshift is not supported with the --addfragments option." 1>>"$progressfile" - exit 1; - fi - fi - - if [ `awk "BEGIN {print( 0.0+\"$spfactor\" < 1.0 )}"` -gt 0 ]; then - printf "\n%s\n" "shiftpenalty must be >1." 1>>"$progressfile" - exit 1; - fi - - if [ `awk "BEGIN {print( 0.0+\"$fixthreshold\" < 0.0 )}"` -gt 0 ]; then - printf "\n%s\n\n" "The 'fix' parameter must be >= 0.0" 1>>"$progressfile" - exit 1; - fi - - if [ `awk "BEGIN {print( 0.0+\"$unalignlevel\" < 0.0 || 0.0+\"$unalignlevel\" > 1.0 )}"` -gt 0 ]; then - printf "\n%s\n\n" "The 'unalignlevel' parameter must be between 0.0 and 1.0" 1>>"$progressfile" - exit 1; - fi - if [ `awk "BEGIN {print( 0.0+\"$unalignlevel\" > 0.0 )}"` -gt 0 ]; then - laof="0" - lexp="0" - pgaof="0" - pgexp="0" - LEXP="0" - GEXP="0" - termgapopt=" " -# if [ $auto -eq 1 -o $fragment -ne 0 -o $iterate -gt 0 ]; then - if [ $fragment -ne 0 ]; then - printf "\n%s\n\n" "At present, the 'unalignlevel > 0' mode is not supported with the --addfragments option." 1>>"$progressfile" - exit 1; - fi - if [ $distance = "parttree" ]; then - printf "\n%s\n\n" "At present, the 'unalignlevel > 0' mode is not supported in the (dp)parttree option." 1>>"$progressfile" - exit 1; - fi - if [ $distance = "localgenaf" ]; then - printf "\n%s\n" "The --genafpair is not supported in the 'unalignlevel > 0' mode." 1>>"$progressfile" - printf "%s\n" "Instead, please try --unalignlevel xx --globalpair," 1>>"$progressfile" - printf "%s\n\n" "which covers the situation for --genafpair (E-INS-i), too." 1>>"$progressfile" - exit 1; - fi -# if [ $distance != "ktuples" -a `awk "BEGIN {print( 0.0+\"$weighti\" > 0.0 )}"` -gt 0 -a $iterate -gt 0 ]; then -# printf "\n%s\n\n" "Please add --weighti 0.0, for now." 1>>"$progressfile" -# exit 1; -# fi - fi - - if [ `awk "BEGIN {print( 0.0+\"$similarityoffset\" != 0.0 && 0.0+\"$unalignlevel\" != 0.0 )}"` -gt 0 ]; then - printf "\n%s\n\n" "Do not simultaneously specify --similaritylevel and --unalignlevel" 1>>"$progressfile" - exit 1; - fi - - if [ `awk "BEGIN {print( 0.0+\"$similarityoffset\" < -1.0 || 0.0+\"$similarityoffset\" > 1.0 )}"` -gt 0 ]; then - printf "\n%s\n\n" "Similarity must be between -1.0 and +1.0" 1>>"$progressfile" - exit 1; - fi - aof=`awk "BEGIN{print 0.0 + \"$similarityoffset\" + $aof}"` - laof=`awk "BEGIN{print 0.0 + \"$similarityoffset\" + $laof}"` - pgaof=`awk "BEGIN{print 0.0 + \"$similarityoffset\" + $pgaof}"` - - - if [ $parallelizationstrategy = "BESTFIRST" -o $parallelizationstrategy = "BAATARI0" ]; then - iteratelimit=254 - else - iteratelimit=16 - fi - if [ $iterate -gt $iteratelimit ]; then #?? - iterate=$iteratelimit - fi - - if [ $rnaalifold -eq 1 ]; then - rnaopt=" -e $rgep -o $rgop -c $weightm -r $weightr -R $rnascoremtx " -# rnaoptit=" -o $rgop -BT -c $weightm -r $weightr -R " - rnaoptit=" -o $rgop -F -c $weightm -r $weightr -R " - elif [ $mccaskill -eq 1 -o $dafs -eq 1 -o $contrafold -eq 1 ]; then - rnaopt=" -o $rgop -c $weightm -r $weightr " -# rnaoptit=" -e $rgep -o $rgop -BT -c $weightm -r $weightr $rnascoremtx " - rnaoptit=" -e $rgep -o $rgop -F -c $weightm -r $weightr $rnascoremtx " - else - rnaopt=" " - rnaoptit=" -F " - fi - -# if [ $algspecified -eq 0 ]; then -# if [ $distance = "parttree" ]; then -# algopt=" -Q " -# algoptit=" " -# else -# algopt=" " -# algoptit=" " -# fi -# fi - - if [ $sprigorous -eq 1 ]; then - algopt=" -@ " - if [ $iterate -gt 0 ]; then - if [ $numthreadsit -eq 0 ]; then - algoptit=" -@ -B -Z -z 1000 " - else - echo "" 1>>"$progressfile" - echo "At present, the combination of --sp and iterative refinement is supported only in a single thread." 1>>"$progressfile" - echo "Please try \"--thread -1 --threadit 0\", which runs the iterative refinment calculation on a single thread." 1>>"$progressfile" - echo "" 1>>"$progressfile" - exit 1; -# algoptit=" -@ -B -z 1000 " - fi - fi - termgapopt=" " - fft=0 - memopt=" -N " - fi - - model="$sbstmodel $kappa $fmodel $nmodel" - - if [ $er -eq 1 ]; then - echo "------------------------------------------------------------------------------" 1>&2 - echo " MAFFT" $version 1>&2 -# echo "" 1>&2 -# echo " Input format: fasta" 1>&2 -# echo "" 1>&2 -# echo " Usage: `basename $0` [options] inputfile > outputfile" 1>&2 - echo " https://mafft.cbrc.jp/alignment/software/" 1>&2 - echo " MBE 30:772-780 (2013), NAR 30:3059-3066 (2002)" 1>&2 -# echo "------------------------------------------------------------------------------" 1>&2 -# echo " % mafft in > out" 1>&2 - echo "------------------------------------------------------------------------------" 1>&2 -# echo "" 1>&2 - echo "High speed:" 1>&2 - echo " % mafft in > out" 1>&2 - echo " % mafft --retree 1 in > out (fast)" 1>&2 - echo "" 1>&2 - echo "High accuracy (for <~200 sequences x <~2,000 aa/nt):" 1>&2 - echo " % mafft --maxiterate 1000 --localpair in > out (% linsi in > out is also ok)" 1>&2 - echo " % mafft --maxiterate 1000 --genafpair in > out (% einsi in > out)" 1>&2 - echo " % mafft --maxiterate 1000 --globalpair in > out (% ginsi in > out)" 1>&2 - echo "" 1>&2 - echo "If unsure which option to use:" 1>&2 - echo " % mafft --auto in > out" 1>&2 - echo "" 1>&2 -# echo "Other options:" 1>&2 - echo "--op # : Gap opening penalty, default: 1.53" 1>&2 - echo "--ep # : Offset (works like gap extension penalty), default: 0.0" 1>&2 - echo "--maxiterate # : Maximum number of iterative refinement, default: 0" 1>&2 - echo "--clustalout : Output: clustal format, default: fasta" 1>&2 - echo "--reorder : Outorder: aligned, default: input order" 1>&2 - echo "--quiet : Do not report progress" 1>&2 - echo "--thread # : Number of threads (if unsure, --thread -1)" 1>&2 - echo "--dash : Add structural information (Rozewicki et al, submitted)" 1>&2 -# echo "" 1>&2 -# echo " % mafft --maxiterate 1000 --localpair in > out (L-INS-i)" 1>&2 -# echo " most accurate in many cases, assumes only one alignable domain" 1>&2 -# echo "" 1>&2 -# echo " % mafft --maxiterate 1000 --genafpair in > out (E-INS-i)" 1>&2 -# echo " works well if many unalignable residues exist between alignable domains" 1>&2 -# echo "" 1>&2 -# echo " % mafft --maxiterate 1000 --globalpair in > out (G-INS-i)" 1>&2 -# echo " suitable for globally alignable sequences " 1>&2 -# echo "" 1>&2 -# echo " % mafft --maxiterate 1000 in > out (FFT-NS-i)" 1>&2 -# echo " accurate and slow, iterative refinement method " 1>&2 -# echo "" 1>&2 -# echo "If the input sequences are long (~1,000,000nt)," 1>&2 -# echo " % mafft --retree 1 --memsave --fft in > out (FFT-NS-1-memsave, new in v5.8)" 1>&2 -# echo "" 1>&2 -# echo "If many (~5,000) sequences are to be aligned," 1>&2 -# echo "" 1>&2 -# echo " % mafft --retree 1 [--memsave] --nofft in > out (NW-NS-1, new in v5.8)" 1>&2 -# echo "" 1>&2 -# echo " --localpair : All pairwise local alignment information is included" 1>&2 -# echo " to the objective function, default: off" 1>&2 -# echo " --globalpair : All pairwise global alignment information is included" 1>&2 -# echo " to the objective function, default: off" 1>&2 -# echo " --op # : Gap opening penalty, default: $defaultgop " 1>&2 -# echo " --ep # : Offset (works like gap extension penalty), default: $defaultaof " 1>&2 -# echo " --bl #, --jtt # : Scoring matrix, default: BLOSUM62" 1>&2 -# echo " Alternatives are BLOSUM (--bl) 30, 45, 62, 80, " 1>&2 -# echo " or JTT (--jtt) # PAM. " 1>&2 -# echo " --nuc or --amino : Sequence type, default: auto" 1>&2 -# echo " --retree # : The number of tree building in progressive method " 1>&2 -# echo " (see the paper for detail), default: $defaultcycle " 1>&2 -# echo " --maxiterate # : Maximum number of iterative refinement, default: $defaultiterate " 1>&2 -# if [ $defaultfft -eq 1 ]; then -# echo " --fft or --nofft: FFT is enabled or disabled, default: enabled" 1>&2 -# else -# echo " --fft or --nofft: FFT is enabled or disabled, default: disabled" 1>&2 -# fi -# echo " --memsave: Memory saving mode" 1>&2 -# echo " (for long genomic sequences), default: off" 1>&2 -# echo " --clustalout : Output: clustal format, default: fasta" 1>&2 -# echo " --reorder : Outorder: aligned, default: input order" 1>&2 -# echo " --quiet : Do not report progress" 1>&2 -# echo "-----------------------------------------------------------------------------" 1>&2 - exit 1; - fi - if [ $sw -eq 1 ]; then - swopt=" -A " - else - swopt=" " - fi - - if [ $distance = "fasta" -o $partdist = "fasta" ]; then - if [ ! "$FASTA_4_MAFFT" ]; then - FASTA_4_MAFFT=`which fasta34` - fi - - if [ ! -x "$FASTA_4_MAFFT" ]; then - echo "" 1>&2 - echo "== Install FASTA ========================================================" 1>&2 - echo "This option requires the fasta34 program (FASTA version x.xx or higher)" 1>&2 - echo "installed in your PATH. If you have the fasta34 program but have renamed" 1>&2 - echo "(like /usr/local/bin/myfasta), set the FASTA_4_MAFFT environment variable" 1>&2 - echo "to point your fasta34 (like setenv FASTA_4_MAFFT /usr/local/bin/myfasta)." 1>&2 - echo "=========================================================================" 1>&2 - echo "" 1>&2 - exit 1 - fi - fi - if [ $distance = "last" -o $distance = "lastmulti" ]; then - if [ ! -x "$prefix/lastal" -o ! -x "$prefix/lastdb" ]; then - echo "" 1>&2 - echo "== Install LAST ============================================================" 1>&2 - echo "LAST (Kielbasa, Wan, Sato, Horton, Frith 2011 Genome Res. 21:487) is required." 1>&2 - echo "http://last.cbrc.jp/" 1>&2 - echo "http://mafft.cbrc.jp/alignment/software/xxxxxxx.html " 1>&2 - echo "============================================================================" 1>&2 - echo "" 1>&2 - exit 1 - fi - fi - if [ $distance = "lara" -o $distance = "slara" ]; then - if [ ! -x "$prefix/mafft_lara" ]; then - echo "" 1>&2 - echo "== Install LaRA =========================================================" 1>&2 - echo "This option requires LaRA (Bauer et al. http://www.planet-lisa.net/)." 1>&2 - echo "The executable have to be renamed to 'mafft_lara' and installed into " 1>&2 - echo "the $prefix directory. " 1>&2 - echo "A configuration file of LaRA also have to be given" 1>&2 - echo "mafft-xinsi --larapair --laraparams parameter_file" 1>&2 - echo "mafft-xinsi --slarapair --laraparams parameter_file" 1>&2 - echo "=========================================================================" 1>&2 - echo "" 1>&2 - exit 1 - fi - if [ ! -s "$laraparams" ]; then - echo "" 1>&2 - echo "== Configure LaRA =======================================================" 1>&2 - echo "A configuration file of LaRA have to be given" 1>&2 - echo "mafft-xinsi --larapair --laraparams parameter_file" 1>&2 - echo "mafft-xinsi --slarapair --laraparams parameter_file" 1>&2 - echo "=========================================================================" 1>&2 - echo "" 1>&2 - exit 1 - fi - fi - if [ $distance = "foldalignlocal" -o $distance = "foldalignglobal" ]; then - if [ ! -x "$prefix/foldalign210" ]; then - echo "" 1>&2 - echo "== Install FOLDALIGN ====================================================" 1>&2 - echo "This option requires FOLDALIGN (Havgaard et al. http://foldalign.ku.dk/)." 1>&2 - echo "The executable have to be renamed to 'foldalign210' and installed into " 1>&2 - echo "the $prefix directory. " 1>&2 - echo "=========================================================================" 1>&2 - echo "" 1>&2 - exit 1 - fi - fi - if [ $distance = "scarna" -o $mccaskill -eq 1 ]; then - if [ ! -x "$prefix/mxscarnamod" ]; then - echo "" 1>&2 - echo "== Install MXSCARNA ======================================================" 1>&2 - echo "MXSCARNA (Tabei et al. BMC Bioinformatics 2008 9:33) is required." 1>&2 - echo "Please 'make' at the 'extensions' directory of the MAFFT source package," 1>&2 - echo "which contains the modified version of MXSCARNA." 1>&2 - echo "http://mafft.cbrc.jp/alignment/software/source.html " 1>&2 - echo "==========================================================================" 1>&2 - echo "" 1>&2 - exit 1 - fi - fi - if [ $distance = "dafs" -o $dafs -eq 1 ]; then - if [ ! -x "$prefix/dafs" ]; then - echo "" 1>&2 - echo "== Install DAFS===========================================================" 1>&2 - echo "DAFS (Sato et al. Journal 2012 issue:page) is required." 1>&2 - echo "http://www.ncrna.org/ " 1>&2 - echo "==========================================================================" 1>&2 - echo "" 1>&2 - exit 1 - fi - fi - if [ $contrafold -eq 1 ]; then - if [ ! -x "$prefix/contrafold" ]; then - echo "" 1>&2 - echo "== Install CONTRAfold ===================================================" 1>&2 - echo "This option requires CONTRAfold" 1>&2 - echo "(Do et al. http://contra.stanford.edu/contrafold/)." 1>&2 - echo "The executable 'contrafold' have to be installed into " 1>&2 - echo "the $prefix directory. " 1>&2 - echo "=========================================================================" 1>&2 - echo "" 1>&2 - exit 1 - fi - fi - -#old -# if [ $treeout -eq 1 ]; then -# parttreeoutopt="-t" -# if [ $cycle -eq 0 ]; then -# treeoutopt="-t -T" -# groupsize=1 -# iterate=0 -# if [ $distance = "global" -o $distance = "local" -o $distance = "localgenaf" -o $distance = "globalgenaf" ]; then -# distance="distonly" -# fi -# else -# treeoutopt="-t" -# fi -# else -# parttreeoutopt=" " -# if [ $cycle -eq 0 ]; then -# treeoutopt="-t -T" -# iterate=0 -# if [ $distance = "global" -o $distance = "local" -o $distance = "localgenaf" -o $distance = "globalgenaf" ]; then -# distance="distonly" -# fi -# else -# treeoutopt=" " -# fi -# fi - -#new - if [ $cycle -eq 0 ]; then - if [ $nodeout -eq 1 ]; then - treeoutopt="-^ -T" - else - treeoutopt="-t -T" - fi - iterate=0 - weighti="0.0" # 2016Jul31, tbfast.c kara idou -# if [ $distance = "global" -o $distance = "local" -o $distance = "localgenaf" -o $distance = "globalgenaf" ]; then # 2012/04, localpair --> local alignment distance -# if [ $distance = "global" ]; then -# distance="distonly" -# fi - if [ $treeout -eq 1 ]; then - parttreeoutopt="-t" - groupsize=1 - else - parttreeoutopt=" " - fi - if [ $distout -eq 1 ]; then - distoutopt="-y -T" - if [ $treeout -eq 0 ]; then - treeoutopt="" - fi - fi - else - if [ $nodeout -eq 1 ]; then - if [ $iterate -gt 0 ]; then - echo "The --nodeout option supports only progressive method (--maxiterate 0) for now." 1>&2 - exit 1 - fi - parttreeoutopt="-t" - treeoutopt="-^" - elif [ $treeout -eq 1 ]; then - parttreeoutopt="-t" - treeoutopt="-t" - else - parttreeoutopt=" " - treeoutopt=" " - fi - if [ $distout -eq 1 ]; then - distoutopt="-y" - fi - fi -# - - formatcheck=`grep -c '^[[:blank:]]\+>' "$TMPFILE/infile" | head -1 ` - if [ $formatcheck -gt 0 ]; then - echo "The first character of a description line must be " 1>&2 - echo "the greater-than (>) symbol, not a blank." 1>&2 - echo "Please check the format around the following line(s):" 1>&2 - grep -n '^[[:blank:]]\+>' "$TMPFILE/infile" 1>&2 - exit 1 - fi - - nseq=`grep -c '^[>|=]' "$TMPFILE/infile" | head -1 ` - if [ $nseq -eq 2 ]; then - cycle=1 - fi - if [ $cycle -gt 3 ]; then - cycle=3 - fi - - if [ $nseq -gt 60000 -a $iterate -gt 1 ]; then # 2014/Oct/22, test - echo "Too many sequences to perform iterative refinement!" 1>&2 - echo "Please use a progressive method." 1>&2 - exit 1 - fi - if [ $distance = "lastmulti" -o $distance = "multi" ]; then - if [ $fragment -eq 0 ]; then - echo 'Specify --addfragments too' 1>&2 - exit 1 - fi - fi - - if [ $fragment -ne 0 ]; then - if [ $pairspecified -eq 0 ]; then - distance="multi" - fi - if [ $distance != "multi" -a $distance != "hybrid" -a $distance != "lastmulti" -a $distance != "local" -a $distance != "last" -a $distance != "ktuples" -a $distance != "ktuplesmulti" ]; then - echo 'Specify --multipair, --lastmultipair, --lastpair, --localpair, --6merpair, --6mermultipair or --hybridpair' 1>&2 - exit 1 - fi - fi - - if [ "$memopt" = " -M -B " -a "$distance" != "ktuples" ]; then - echo "Impossible" 1>&2 - exit 1 - fi - - if [ $distance = "parttree" ]; then - if [ "$mergetable" != "/dev/null" ]; then - echo "The combination of (dp)parttree and merge is Impossible. " 1>&2 - exit 1 - fi - if [ $addfile != "/dev/null" ]; then - echo "The combination of (dp)parttree and add(fragments) is Impossible. " 1>&2 - exit 1 - fi - if [ $seed != "x" -o $seedtable != "x" ]; then - echo "Impossible" 1>&2 - exit 1 - fi - if [ $iterate -gt 1 ]; then - echo "Impossible" 1>&2 - exit 1 - fi - if [ $outorder = "aligned" ]; then - outorder="input" - fi - outorder="input" # partorder ga kiku - if [ $partdist = "localalign" ]; then - splitopt=" -U " # -U -l -> fast - cycle=1 - elif [ $partdist = "fasta" ]; then - splitopt=" -S " - cycle=1 - else - splitopt=" " - fi - fi - - - if [ \( $distance = "ktuples" -o $distance = "ktuplesmulti" \) -a \( $seed = "x" -a $seedtable = "x" -a $ownlist = "/dev/null" -a $pdblist = "/dev/null" -a $enrichstr -eq 0 -a $newdash -eq 0 \) ]; then - localparam="" - weighti="0.0" - elif [ \( $distance = "ktuples" -o $distance = "ktuplesmulti" \) -a \( $seed != "x" -o $seedtable != "x" -o $ownlist != "/dev/null" -o $pdblist != "/dev/null" -o $enrichstr -eq 1 -o $newdash -eq 1 \) ]; then - if [ $cycle -lt 2 ]; then - cycle=2 # disttbfast ha seed hi-taiou # chuui 2014Aug21 - fi - if [ $iterate -lt 2 ]; then - echo "############################################################################" 1>&2 - echo "# Warning:" 1>&2 - echo "# Progressive alignment method is incompatible with the --seed option." 1>&2 - echo "# Automatically switched to the iterative refinement method." 1>&2 - echo "# " 1>&2 - echo "# Also consider using the '--add' option, which is compatible with" 1>&2 - echo "# the progressive method and FASTER than the '--seed' option." 1>&2 - echo "# Usage is:" 1>&2 - echo "# % mafft --add newSequences existingAlignment > output" 1>&2 - echo "############################################################################" 1>&2 - iterate=2 - fi - localparam="-l "$weighti - elif [ $distance = "parttree" ]; then - localparam="" - weighti="0.0" - if [ $groupsize -gt -1 ]; then - cycle=1 - fi - else -# localparam="-B -l "$weighti # weighti=0 demo bunkatsu nashi - localparam="-l "$weighti # -B (bunkatsunashi) ha dvtditr.c de taiou (17/Jan/15) - if [ $cycle -gt 1 ]; then # 09/01/08 - cycle=1 - fi - fi - - - if [ $distance = "localgenaf" -o $distance = "globalgenaf" ]; then - aof="0.000" - if [ $oldgenafparam -ne 1 ]; then - laof="0.0" - lexp="0.0" -# LEXP="0.0" # default = 0.0 - usenaivepairscore="-Z" - fi - fi - - -# if [ $nseq -gt 5000 ]; then -# fft=0 -# fi - if [ $forcefft -eq 1 ]; then - param_fft=" -G " - fft=1 - elif [ $fft -eq 1 ]; then - param_fft=" -F " - else - param_fft=" " - fi - - if [ $seed != "x" -a $seedtable != "x" ]; then - echo 'Use either one of seedtable and seed. Not both.' 1>&2 - exit 1 - fi - if [ $f2clext = "-E" -a $anysymbol -gt 0 ]; then - echo '' 1>&2 - echo 'The combination of --text and ( --anysymbol or --preservecase ) is impossible.' 1>&2 - echo '' 1>&2 - exit 1 - fi - -# if [ $f2clext = "-E" -a $scorematrix != "/dev/null" ]; then -# echo '' 1>&2 -# echo 'At present, the combination of --text and (--aamatrix) is impossible.' 1>&2 -# echo '' 1>&2 -# exit 1 -# fi - - memsavetree=0 - if [ $treeext != "none" ]; then - if [ $distance == "ktuples" ]; then - treein=1 - treeinopt=" -U " - if [ $treeext == "randomchain" ]; then - echo "shuffle $randomseed" > "$TMPFILE/_guidetree" - cycle=1 # disttbfast.c dem shitei - elif [ $treeext == "pileup" ]; then - echo "pileup" > "$TMPFILE/_guidetree" - cycle=1 # disttbfast. shitei - elif [ $treeext == "memsavetree" ]; then - echo "very compact" > "$TMPFILE/_guidetree" - memsavetree=1 - elif [ $treeext == "memsavetreex" ]; then - echo "compact " "$initialramusage" > "$TMPFILE/_guidetree" - memsavetree=1 - elif [ $treeext == "stepadd" ]; then - echo "stepadd" > "$TMPFILE/_guidetree" - memsavetree=1 - elif [ $treeext == "youngestlinkage" ]; then - echo "youngestlinkage" > "$TMPFILE/_guidetree" - memsavetree=1 - else - echo "error in mafft.tmpl" - exit - fi - else # globalpair, localpair, genafpair, oldgenafpair -# treein, treeinopt ha kimaranai - if [ $treeext == "memsavetree" -o $treeext == "stepadd" ]; then - memsavetree=1 - else - echo "With globalpair, localpair or genafpair," 1>>"$progressfile" - echo "Use --large, --minimumlinkage, --averagelinkage or --mixedlinkage." 1>>"$progressfile" - echo "--$treeext is supported only with --6merpair." 1>>"$progressfile" - echo '' 1>>"$progressfile" - exit - fi - fi - if [ $iterate -gt 0 ]; then - echo 'Iterative refinment is not supported for --large or --'$treeext 1>>"$progressfile" - echo '' 1>>"$progressfile" - exit 1 - fi - if [ $fragment -ne 0 ]; then - echo '--addfragments, --addfull or --addlong is not yet supported for --large or --'$treeext 1>>"$progressfile" - echo "Use --add newsequences --$treeext" 1>>"$progressfile" - echo "Or, --addfragments (long, full) newsequences, without --"$treeext 1>>"$progressfile" - echo '' 1>>"$progressfile" - exit 1 - fi - if [ "$mergetable" != "/dev/null" ]; then # 2018/Mar/2 - echo '--merge is not yet supported for --large or --'$treeext 1>>"$progressfile" - echo "Use --merge without --"$treeext 1>>"$progressfile" - echo '' 1>>"$progressfile" - exit 1 - fi - fi - - - - if [ $nadd -gt "0" ]; then - if [ $fragment -eq "1" ]; then - addarg="$addarg0 $nadd -g -0.01" - addsinglearg="" - cycle=1 # chuui 2014Aug25 - iterate=0 - elif [ $fragment -eq "-1" ]; then - addarg="$addarg0 $nadd" - addsinglearg="-V" # allowlongadds, 2014/04/02 - cycle=1 # chuui 2014Aug25 - iterate=0 - elif [ $fragment -eq "-2" ]; then - addarg="$addarg0 $nadd" - addsinglearg="-V" # allowlongadds + smoothing - add2ndhalfarg=$add2ndhalfarg" -p " - cycle=1 # chuui 2014Aug25 - usenaivepairscore="-Z" # 2015Jun01 - laof=0.0 # 2015Jun01 - lexp=0.0 # 2015Jun01 - iterate=0 - elif [ $fragment -eq "-3" ]; then - addarg="$addarg0 $nadd" - addsinglearg="-x" # add to top, 2021/12/31 - cycle=1 # chuui 2014Aug25 - iterate=0 - elif [ $fragment -eq "-4" ]; then - addarg="$addarg0 $nadd" - addsinglearg="-s" # add to root, 2023/2/11 - cycle=1 # chuui 2014Aug25 - iterate=0 - else - addarg="$addarg0 $nadd" - addsinglearg="" -# iterate=1 # iterate ha shitei dori - bunkatsuopt=" -B " # fftnsi demo bunktasu shinai - if [ "$add2ndhalfarg" != " " ]; then - if [ $auto -eq 1 -o $iterate -gt 0 ]; then -# echo '' 1>>"$progressfile" -# echo 'The --keeplength and --mapout options are not supported' 1>>"$progressfile" -# echo 'with the --auto or --maxiterate >0 options.' 1>>"$progressfile" -# echo 'Use the --maxiterate 0 option (= progressive method).' 1>>"$progressfile" -# echo '' 1>>"$progressfile" -# exit 1 - iterate=0 - fi - fi - fi - - -# cycle=1 # chuui 2014Aug19 -# iterate=0 -# treealg=" -q " ## 2012/01/24 ## removed 2012/02/06 - else - if [ "$add2ndhalfarg" != " " ]; then - echo '' 1>>"$progressfile" - echo 'The --keeplength and --mapout options are supported' 1>>"$progressfile" - echo 'only with --add, --addfragments or --addlong.' 1>>"$progressfile" - echo '' 1>>"$progressfile" - exit 1 - fi - fi - - if [ "$codonposfile" != "/dev/null" -o "$codonscorefile" != "/dev/null" ]; then - if [ $nadd -eq "0" -o $fragment -eq "0" ]; then - echo '' 1>>"$progressfile" - echo "'--codonpos' and '--codonscore' options are supported only with the '--6merpair --addfragments' option." 1>>"$progressfile" - echo '' 1>>"$progressfile" - exit 1 - fi - if [ $distance != "ktuples" ]; then # ato de taiou - echo '' 1>>"$progressfile" - echo "'--codonpos' and '--codonscore' options are supported only with the '--6merpair --addfragments' option, at this point." 1>>"$progressfile" - echo '' 1>>"$progressfile" - exit 1 - fi - fi - - - if [ -z "$localparam" -a $fragment -eq 0 -a $distance != "parttree" ]; then -# echo "use disttbfast" -# echo cycle = $cycle - cycletbfast=1 # tbfast wo jikkou shinai - cycledisttbfast=$cycle # disttbfast ni -E cycle wo watasu - if [ $cycledisttbfast -eq 0 ]; then # --treeout de tsukau - cycledisttbfast=1 - fi - else -# echo "use tbfast" -# echo cycle = $cycle - cycletbfast=$cycle # 1 ijou nara jikkou - cycledisttbfast=1 # disttbfast ha ikkai dake - fi - -# echo localparam= -# echo $localparam -# echo cycletbfast= -# echo $cycletbfast -# echo cycledisttbfast= -# echo $cycledisttbfast - -#exit - - if [ $adjustdirection -gt 0 -a $seed != "x" ]; then - echo '' 1>&2 - echo 'The combination of --adjustdirection(accurately) and --seed is not supported.' 1>&2 - echo '' 1>&2 - exit 1 - fi - - - if [ $mccaskill -eq 1 -o $dafs -eq 1 -o $rnaalifold -eq 1 -o $contrafold -eq 1 ]; then - if [ $distance = "ktuples" ]; then - echo 'Not supported.' 1>&2 - echo 'Please add --globalpair, --localpair, --scarnapair, --dafspair' 1>&2 - echo '--larapair, --slarapair, --foldalignlocalpair or --foldalignglobalpair' 1>&2 - exit 1 - fi - if [ $f2clext = "-E" ]; then - echo '' 1>&2 - echo 'For RNA alignment, the --text mode is impossible.' 1>&2 - echo '' 1>&2 - exit 1 - fi - fi - -# cycle ga atode henkou sareru node koko de strategy no namae wo kimeru. -# kokokara - if [ $treeext = "pileup" ]; then - strategy="Pileup-" - elif [ $treeext = "randomchain" ]; then - strategy="Randomchain-" - elif [ $mccaskill -eq 1 -o $dafs -eq 1 -o $rnaalifold -eq 1 -o $contrafold -eq 1 ]; then - if [ $distance = "scarna" -o $distance = "dafs" -o $distance = "lara" -o $distance = "slara" -o $distance = "foldalignlocal" -o $distance = "foldalignglobal" ]; then - strategy="X-" - elif [ $distance = "global" -o $distance = "local" -o $distance = "localgenaf" -o "globalgenaf" ]; then - strategy="Q-" - fi - elif [ $distance = "fasta" -a $sw -eq 0 ]; then - strategy="F-" - elif [ $distance = "fasta" -a $sw -eq 1 ]; then - strategy="H-" - elif [ $distance = "blast" ]; then - strategy="B-" - elif [ $distance = "global" -o $distance = "distonly" ]; then - strategy="G-" - elif [ $distance = "local" ]; then - strategy="L-" - elif [ $distance = "last" ]; then - strategy="Last-" - elif [ $distance = "hybrid" ]; then - strategy="Hybrid-" - elif [ $distance = "multi" ]; then - strategy="Multi-" - elif [ $distance = "lastmulti" ]; then - strategy="LastMulti-" - elif [ $distance = "localgenaf" ]; then - strategy="E-" - elif [ $distance = "globalgenaf" ]; then - strategy="K-" - elif [ $fft -eq 1 ]; then - strategy="FFT-" - else - strategy="NW-" - fi - if [ $memsavetree -eq 1 ]; then - strategy=$strategy"large-" - fi -# if [ `echo "$weighti>0.0" | bc` -gt 0 ]; then - if [ `awk "BEGIN {print(0.0+\"$weighti\">0.0)}"` -gt 0 ]; then - strategy=$strategy"I" - fi - strategy=$strategy"NS-" - if [ $iterate -gt 0 ]; then - strategy=$strategy"i" - elif [ $distance = "parttree" ]; then - if [ $partdist = "fasta" ]; then - strategy=$strategy"FastaPartTree-"$cycle - elif [ $partdist = "localalign" ]; then - strategy=$strategy"DPPartTree-"$cycle - else - strategy=$strategy"PartTree-"$cycle - fi - elif [ $fragment -eq 1 ]; then - strategy=$strategy"fragment" - elif [ $fragment -eq -1 ]; then - strategy=$strategy"full" - elif [ $fragment -eq -2 ]; then - strategy=$strategy"long" - elif [ $fragment -eq -3 ]; then - strategy=$strategy"top" - else - strategy=$strategy$cycle - fi - - explanation='?' - performance='Not tested.' - if [ $strategy = "F-INS-i" ]; then - explanation='Iterative refinement method (<'$iterate') with LOCAL pairwise alignment information' - performance='Most accurate, but very slow' - elif [ $strategy = "L-INS-i" ]; then - explanation='Iterative refinement method (<'$iterate') with LOCAL pairwise alignment information' - performance='Probably most accurate, very slow' - elif [ $strategy = "E-INS-i" ]; then - explanation='Iterative refinement method (<'$iterate') with LOCAL pairwise alignment with generalized affine gap costs (Altschul 1998)' - performance='Suitable for sequences with long unalignable regions, very slow' - elif [ $strategy = "G-INS-i" ]; then - explanation='Iterative refinement method (<'$iterate') with GLOBAL pairwise alignment information' - performance='Suitable for sequences of similar lengths, very slow' - elif [ $strategy = "X-INS-i" ]; then - explanation='RNA secondary structure information is taken into account.' - performance='For short RNA sequences only, extremely slow' - elif [ $strategy = "F-INS-1" ]; then - explanation='Progressive method incorporating LOCAL pairwise alignment information' - elif [ $strategy = "L-INS-1" ]; then - explanation='Progressive method incorporating LOCAL pairwise alignment information' - elif [ $strategy = "G-INS-1" ]; then - explanation='Progressive method incorporating GLOBAL pairwise alignment information' - elif [ $strategy = "FFT-NS-i" -o $strategy = "NW-NS-i" ]; then - explanation='Iterative refinement method (max. '$iterate' iterations)' - if [ $iterate -gt 2 ]; then - performance='Accurate but slow' - else - performance='Standard' - fi - elif [ $strategy = "FFT-NS-2" -o $strategy = "NW-NS-2" ]; then - explanation='Progressive method (guide trees were built '$cycle' times.)' - performance='Fast but rough' - elif [ $strategy = "FFT-NS-1" -o $strategy = "NW-NS-1" ]; then - explanation='Progressive method (rough guide tree was used.)' - performance='Very fast but very rough' - fi - - if [ $outputformat = "clustal" -a $outorder = "aligned" ]; then - outputopt=" -c $strategy -r $TMPFILE/order $f2clext " - elif [ $outputformat = "clustal" -a $outorder = "input" ]; then - outputopt=" -c $strategy $f2clext " - elif [ $outputformat = "phylip" -a $outorder = "aligned" ]; then - outputopt=" -y -r $TMPFILE/order " - elif [ $outputformat = "phylip" -a $outorder = "input" ]; then - outputopt=" -y " - elif [ $outputformat = "pir" -a $outorder = "aligned" ]; then - outputopt=" -f -l $linelength -r $TMPFILE/order " - else - outputopt="-f -l $linelength" - fi - - if [ $newdash_originalsequenceonly -eq 1 ]; then - outputopt="$outputopt -d " - fi -# kokomade - - - - pushd "$TMPFILE" > /dev/null - - cat /dev/null > pre - -# echo "nseq = " $nseq 1>>"$progressfile" -# echo "distance = " $distance 1>>"$progressfile" -# echo "iterate = " $iterate 1>>"$progressfile" -# echo "cycle = " $cycle 1>>"$progressfile" - - - if [ $anysymbol -eq 1 ]; then - mv infile orig - "$prefix/replaceu" $seqtype -i orig > infile 2>>"$progressfile" || exit 1 - fi - - if [ $mergetable != "/dev/null" ]; then - if [ $nadd -gt "0" ]; then - echo "Impossible" 1>&2 - exit 1 - fi -# if [ $seed != "x" -o $seedtable != "x" ]; then -# echo "This version does not support the combination of merge and seed." 1>&2 -# exit 1 -# fi -# iterate=0 # 2013/04/16 - mergearg="-H $seedoffset" - fi - - if [ $adjustdirection -gt 0 ]; then - if [ $fragment -ne 0 ]; then - fragarg="-F" # - else - fragarg="-F" # 2014/02/06, do not consider other additional sequences, even in the case of --add - fi - if [ $adjustdirection -eq 1 ]; then - "$prefix/makedirectionlist" $fragarg -C $numthreads -m -I $nadd -i infile -t 0.00 -r 5000 -o a > _direction 2>>"$progressfile" - elif [ $adjustdirection -eq 2 ]; then - "$prefix/makedirectionlist" $fragarg -C $numthreads -m -I $nadd -i infile -t 0.00 -r 100 -o a -d > _direction 2>>"$progressfile" - fi - "$prefix/setdirection" $mergearg -d _direction -i infile > infiled 2>>"$progressfile" || exit - mv infiled infile - if [ $anysymbol -eq 1 ]; then - "$prefix/setdirection" $mergearg -d _direction -i orig -r > origd 2>>"$progressfile" || exit - mv origd orig - fi - fi - - if [ $seed != "x" -o $seedtable != "x" ]; then - if [ $pdblist != "/dev/null" -o $ownlist != "/dev/null" ]; then - echo "The combination of --seed and (--pdbidlist or --pdbfilelist) is impossible." 1>>"$progressfile" - exit 1 - fi -# if [ $enrich -eq 1 ]; then -# echo "The combination of --seed and (--enrich, --enrichseq or --enrichstr) is impossible at present." 1>>"$progressfile" -# exit 1 -# fi - - if [ $newdash -eq 1 ]; then - echo "The combination of --seed and --dash is impossible at present." 1>>"$progressfile" - exit 1 - fi - fi - - -# if [ $enrich -eq 1 ]; then -# if [ $ownlist != "/dev/null" ]; then -# echo "Warning: Sequence homologs of the structures given with the --pdbfilelist option cannot be collected.\n" 1>>"$progressfile" -# fi -# echo "SEEKQUENCER (http://sysimm.ifrec.osaka-u.ac.jp/seekquencer/) is" 1>>"$progressfile" -# if [ $pdblist != "/dev/null" ]; then -# echo "collecting homoplogs of the input sequences and the structures given with the --pdbidlist option." 1>>"$progressfile" -# perl "$prefix/seekquencer_premafft.pl" $seektarget -run thread -trd 2 -seqd uniref90 -blim 1000 -noin -seqf infile -idf pdblist -out seekout -mod mafftash-split 2>>"seekerr" -# seekres="$?" -# else -# echo "collecting homologs of the input sequences." 1>>"$progressfile" -# perl "$prefix/seekquencer_premafft.pl" $seektarget -run thread -trd 2 -seqd uniref90 -blim 1000 -noin -seqf infile -out seekout -mod mafftash-split 2>>"seekerr" -# seekres="$?" -# fi -# cat seekerr 1>>"$progressfile" -# -# if [ $seekres -ne "0" ]; then -# echo "Error in SEEKQUENCER" 1>>"$progressfile" -# exit 1; -# fi -# echo "Done." 1>>"$progressfile" -# -# if [ $enrichseq -eq 1 ]; then -## cat seekout.seq >> infile -# if [ $anysymbol -eq 1 ]; then -# "$prefix/replaceu" $seqtype -i seekout.seq -o $nseq >> infile -# cat seekout.seq >> orig -# else -# "$prefix/replaceu" $seqtype -i seekout.seq | sed 's/_os_[0-9]*_oe_//' >> infile -# fi -# -# fi -# if [ $enrichstr -eq 1 ]; then -# nseekstr=`wc -l < seekout.str` -# if [ $nseekstr -gt 1 ]; then -# cat seekout.str >> pdblist -# pdblist="tsukaimasu" -# fi -# fi -# fi - - if [ $seed != "x" ]; then - mv infile infile2 - if [ $anysymbol -eq 1 ]; then - mv orig orig2 - cat /dev/null > orig - fi - cat /dev/null > infile - cat /dev/null > hat3.seed - seedoffset=0 -# echo "seednseq="$seednseq -# echo "seedoffset="$seedoffset - set $seednseq >> "$progressfile" -# echo $# - while [ $# -gt 1 ] - do - shift -# echo "num="$# - - if [ $anysymbol -eq 1 ]; then - cat seed$# >> orig - "$prefix/replaceu" $seqtype -i seed$# -o $seedoffset > clean 2>>"$progressfile" || exit 1 - mv clean seed$# - fi - "$prefix/multi2hat3s" -t $nseq -o $seedoffset -i seed$# >> infile 2>>"$progressfile" || exit 1 - cat hat3 >> hat3.seed -# echo "$1" - seedoffset=`expr $seedoffset + $1` -# echo "$1" -# echo "seedoffset="$seedoffset - done; -# echo "seedoffset="$seedoffset - if [ $anysymbol -eq 1 ]; then - "$prefix/replaceu" $seqtype -i orig2 -o $seedoffset >> infile 2>>"$progressfile" || exit 1 # yarinaoshi - cat orig2 >> orig - else - cat infile2 >> infile - fi - elif [ $seedtable != "x" ]; then - cat _seedtablefile > hat3.seed - elif [ $newdash -eq 1 ]; then - seemstobe=`"$prefix/countlen" -i infile | awk '{print $6}'` - if [ $seemstobe = "d" -a "x$seqtype" != "x-P" ]; then - echo "" 1>>"$progressfile" - echo "Error: This data seems to be nucleotide sequences." 1>>"$progressfile" - echo "Add the --amino flag if this is surely protein." 1>>"$progressfile" - echo "" 1>>"$progressfile" - exit 1; - fi - if [ $anysymbol -eq 1 ]; then - mv orig infile # replaceu wo mukouka - fi -# sed 's/-//g' infile > dashin # gap nozoku - awk '{if(/^>/)print; else {gsub( /-/,"" ); print;}}' infile > dashin - - if [ ! -x "$prefix/dash_client" -o ! -x "$prefix/dash_client" ]; then - echo "" 1>&2 - echo "== Install DASH client =====================================================" 1>&2 - echo "To use this feature, uncomment the following line in Makefile" 1>&2 - echo "DASH_CLIENT = dash_client" 1>&2 - echo "and re-compile the source." 1>&2 - echo "Note that it requires the 'Go' compiler." 1>&2 - echo "============================================================================" 1>&2 - echo "" 1>&2 - exit 1 - fi - - echo "Calling DASH (https://sysimm.org/dash/)" 1>>"$progressfile" - "$prefix/dash_client" -url "$dashserver" -i dashin -sequences dashsequences -hat3 hat3.seed 1>>"$progressfile" - dashres="$?" - if [ $dashres -ne "0" ]; then - echo "Error in DASH" 1>>"$progressfile" - echo "To enable this feature, compile with DASH_CLIENT=dash_client. Go compiler is necessary." 1>>"$progressfile" - exit 1; - fi - - if [ $exclude_ho -eq 1 ]; then # amari yokunai - awk 'BEGIN{out=1} !/^>_addedbymaffte_/{if(out) print; out=1} /^>_addedbymaffte_/{out=0}' dashsequences | sed 's/>DASH_/>DASH|/' > ho_excluded - mv ho_excluded dashsequences - fi - - if [ "$mergetable" != "/dev/null" ]; then # 2020/Apr/30 - ndash=`grep -c '>DASH_' dashsequences | head -1` -# echo "ndash = " $ndash - awk "{for( i=1;i<=NF;i++){if(0+\$i==0)break; printf( \"%d \", $ndash+\$i); } print \"\" }" _subalignmentstable > _subalignmentstableshifted - mv _subalignmentstableshifted _subalignmentstable - cp dashsequences dashsequences.bk - awk "BEGIN{nout=0} {if(\$1~/^>/) nout++; if( nout <= $ndash ) print;}" dashsequences > infile2 - cat infile >> infile2 - cp infile2 dashsequences - fi - - sed 's/>DASH_/>DASH|/' dashsequences > renamed - mv renamed dashsequences - echo "Done." 1>>"$progressfile" -# cat hat3.seed - seedoffset=`grep -c '^[>|=]' dashsequences | head -1 ` - echo "# of structures = " 1>>"$progressfile" - echo $seedoffset 1>>"$progressfile" - if [ $anysymbol -eq 1 ]; then - cat dashsequences >> orig - "$prefix/replaceu" $seqtype -i dashsequences -o 0 > clean 2>>"$progressfile" || exit 1 - mv clean infile - -# "$prefix/replaceu" $seqtype -i orig2 -o $seedoffset >> infile 2>>"$progressfile" || exit 1 # yarinaoshi -# cat orig2 >> orig - else - cat dashsequences > infile -# cat infile2 >> infile - fi - else - cat /dev/null > hat3.seed - fi -# cat hat3.seed - - if [ $mccaskill -eq 1 ]; then - "$prefix/mccaskillwrap" -s -C $numthreads -d "$prefix" -i infile > hat4 2>>"$progressfile" || exit 1 - elif [ $dafs -eq 1 ]; then - "$prefix/mccaskillwrap" -G -C $numthreads -d "$prefix" -i infile > hat4 2>>"$progressfile" || exit 1 - elif [ $contrafold -eq 1 ]; then - "$prefix/contrafoldwrap" -d "$prefix" -i infile > hat4 2>>"$progressfile" || exit 1 - fi - if [ $distance = "fasta" ]; then - "$prefix/dndfast7" $swopt < infile > /dev/null 2>>"$progressfile" || exit 1 - cat hat3.seed hat3 > hatx - mv hatx hat3 - "$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1 - elif [ $distance = "blast" ]; then - "$prefix/dndblast" < infile > /dev/null 2>>"$progressfile" || exit 1 - cat hat3.seed hat3 > hatx - mv hatx hat3 - "$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1 - elif [ $distance = "foldalignlocal" ]; then - "$prefix/pairlocalalign" -C $numthreads $seqtype $foldalignopt $model -g $lexp -f $lgop -Q $spfactor -h $laof -H -d "$prefix" < infile > /dev/null 2>>"$progressfile" || exit 1 - cat hat3.seed hat3 > hatx - mv hatx hat3 - "$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1 - elif [ $distance = "foldalignglobal" ]; then - "$prefix/pairlocalalign" -C $numthreads $seqtype $foldalignopt $model -g $pgexp -f $pggop -Q $spfactor -h $pgaof -H -o -global -d "$prefix" < infile > /dev/null 2>>"$progressfile" || exit 1 - cat hat3.seed hat3 > hatx - mv hatx hat3 - "$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1 - elif [ $distance = "slara" ]; then - "$prefix/pairlocalalign" -C $numthreads -p $laraparams $seqtype $model -f $lgop -Q $spfactor -T -d "$prefix" < infile > /dev/null 2>>"$progressfile" || exit 1 - cat hat3.seed hat3 > hatx - mv hatx hat3 - "$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1 - elif [ $distance = "lara" ]; then - "$prefix/pairlocalalign" -C $numthreads -p $laraparams $seqtype $model -f $lgop -Q $spfactor -B -d "$prefix" < infile > /dev/null 2>>"$progressfile" || exit 1 - cat hat3.seed hat3 > hatx - mv hatx hat3 - "$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1 - elif [ $distance = "scarna" ]; then -# "$prefix/pairlocalalign" -C $numthreads $seqtype $model -f $pggop -Q $spfactor -s -d "$prefix" < infile > /dev/null 2>>"$progressfile" || exit 1 -# cat hat3.seed hat3 > hatx -# mv hatx hat3 -# "$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1 - "$prefix/tbfast" _ -C $numthreads $seqtype $model -f $pggop -Q $spfactor -s -d "$prefix" _ -+ $iterate -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1 - elif [ $distance = "dafs" ]; then - "$prefix/pairlocalalign" -C $numthreads $seqtype $model -f $pggop -Q $spfactor -G -d "$prefix" < infile > /dev/null 2>>"$progressfile" || exit 1 - cat hat3.seed hat3 > hatx - mv hatx hat3 - "$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1 - elif [ $distance = "global" -a $memsavetree -eq 1 ]; then - if [ "$mpiscript" != "/dev/null" ]; then - sh $mpiscript "$prefix/nodepair_mpi" $lhlimit -u $unalignlevel $localparam $seqtype $model -g $pgexp -f $pggop -Q $spfactor -h $pgaof -A $usenaivepairscore $focusarg $treeinopt $treeoutopt -i infile > /dev/null 2>>"$progressfile" || exit 1 - else - "$prefix/nodepair" $lhlimit -u $unalignlevel $localparam -C $numthreads $seqtype $model -g $pgexp -f $pggop -Q $spfactor -h $pgaof -A $usenaivepairscore $focusarg $treeinopt $treeoutopt -i infile > /dev/null 2>>"$progressfile" || exit 1 - fi - echo 'nodepair' > _guidetree - "$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt -U $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg $focusarg < infile > /dev/null 2>>"$progressfile" || exit 1 - elif [ $distance = "local" -a $memsavetree -eq 1 ]; then - if [ "$mpiscript" != "/dev/null" ]; then - sh $mpiscript "$prefix/nodepair_mpi" $lhlimit -u $unalignlevel $localparam $seqtype $model -g $lexp -f $lgop -Q $spfactor -h $laof -L $usenaivepairscore $focusarg $treeinopt $treeoutopt -i infile > /dev/null 2>>"$progressfile" || exit 1 - else - "$prefix/nodepair" $lhlimit -u $unalignlevel $localparam -C $numthreads $seqtype $model -g $lexp -f $lgop -Q $spfactor -h $laof -L $usenaivepairscore $focusarg $treeinopt $treeoutopt -i infile > /dev/null 2>>"$progressfile" || exit 1 - fi - - echo 'nodepair' > _guidetree - "$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt -U $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg $focusarg < infile > /dev/null 2>>"$progressfile" || exit 1 - elif [ $distance = "localgenaf" -a $memsavetree -eq 1 ]; then - "$prefix/nodepair" $lhlimit -u $unalignlevel $localparam -C $numthreads $seqtype $model -g $lexp -f $lgop -Q $spfactor -h $laof -O $LGOP -E $LEXP -N $usenaivepairscore $focusarg $treeinopt $treeoutopt -i infile > /dev/null 2>>"$progressfile" || exit 1 - echo 'nodepair' > _guidetree - "$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt -U $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg $focusarg < infile > /dev/null 2>>"$progressfile" || exit 1 - elif [ $distance = "global" -a $memsavetree -eq 0 ]; then - "$prefix/tbfast" _ -u $unalignlevel $localparam -C $numthreads $seqtype $model -g $pgexp -f $pggop -Q $spfactor -h $pgaof -A $usenaivepairscore $focusarg _ -+ $iterate -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg $focusarg < infile > /dev/null 2>>"$progressfile" || exit 1 - - elif [ $distance = "local" -a $memsavetree -eq 0 ]; then - if [ $fragment -ne 0 ]; then - "$prefix/pairlocalalign" $localparam $addarg -C $numthreads $seqtype $model -g $lexp -f $lgop -Q $spfactor -h $laof -L $usenaivepairscore < infile > /dev/null 2>>"$progressfile" || exit 1 - cat hat3.seed hat3 > hatx - mv hatx hat3 - "$prefix/addsingle" $codonposopt $codonscoreopt -Q 100 $legacygapopt -O $outnum $addsinglearg $addarg $add2ndhalfarg -C $numthreads $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h $aof $param_fft $localparam $algopt $treealg < infile > /dev/null 2>>"$progressfile" || exit 1 - else - "$prefix/tbfast" _ -u $unalignlevel $localparam -C $numthreads $seqtype $model -g $lexp -f $lgop -Q $spfactor -h $laof -L $usenaivepairscore $focusarg _ -+ $iterate -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg $focusarg < infile > /dev/null 2>>"$progressfile" || exit 1 - fi - elif [ $distance = "globalgenaf" ]; then - "$prefix/pairlocalalign" -u $unalignlevel $localparam -C $numthreads $seqtype $model -g $pgexp -f $pggop -Q $spfactor -h $pgaof -O $GGOP -E $GEXP -K $usenaivepairscore < infile > /dev/null 2>>"$progressfile" || exit 1 - cat hat3.seed hat3 > hatx - mv hatx hat3 - "$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1 - elif [ $distance = "localgenaf" -a $memsavetree -eq 0 ]; then - "$prefix/tbfast" _ -u $unalignlevel $localparam -C $numthreads $seqtype $model -g $lexp -f $lgop -Q $spfactor -h $laof -O $LGOP -E $LEXP -N $usenaivepairscore $focusarg _ -+ $iterate -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg $focusarg < infile > /dev/null 2>>"$progressfile" || exit 1 - elif [ $distance = "last" ]; then - if [ $fragment -ne 0 ]; then - "$prefix/pairlocalalign" $addarg -C $numthreads $seqtype $model -e $last_e -w $last_m -g $lexp -f $lgop -Q $spfactor -h $laof -R $last_subopt $last_once -d "$prefix" < infile > /dev/null 2>>"$progressfile" || exit 1 - cat hat3.seed hat3 > hatx - mv hatx hat3 - "$prefix/addsingle" $codonposopt $codonscoreopt -Q 100 $legacygapopt -O $outnum $addsinglearg $addarg $add2ndhalfarg -C $numthreads $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h $aof $param_fft $localparam $algopt $treealg < infile > /dev/null 2>>"$progressfile" || exit 1 - else - "$prefix/pairlocalalign" -C $numthreads $seqtype $model -e $last_e -w $last_m -g $lexp -f $lgop -Q $spfactor -h $laof -R $last_subopt $last_once -d "$prefix" < infile > /dev/null 2>>"$progressfile" || exit 1 -# addarg wo watasanai - cat hat3.seed hat3 > hatx - mv hatx hat3 - "$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1 - fi - elif [ $distance = "lastmulti" ]; then - "$prefix/dndpre" $model -M 2 $addarg -C $numthreads $seqtype $model -g $lexp -f $lgop -Q $spfactor -h $laof < infile > /dev/null 2>>"$progressfile" || exit 1 - mv hat2 hat2i - "$prefix/pairlocalalign" $addarg -C $numthreads $seqtype $model -e $last_e -w $last_m -g $lexp -f $lgop -Q $spfactor -h $laof -r $last_subopt $last_once -d "$prefix" < infile > /dev/null 2>>"$progressfile" || exit 1 - cat hat3.seed hat3 > hatx - mv hat2 hat2n - mv hatx hat3 - if [ $fragment -ne 0 ]; then - "$prefix/addsingle" $codonposopt $codonscoreopt -Q 100 $legacygapopt -d -O $outnum $addsinglearg $addarg $add2ndhalfarg -C $numthreads $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h $aof $param_fft $localparam $algopt $treealg < infile > /dev/null 2>>"$progressfile" || exit 1 - else - echo "Impossible" 1>&2 - exit 1 - fi - elif [ $distance = "multi" ]; then - "$prefix/dndpre" $model -M 2 $addarg -C $numthreads $seqtype $model -g $lexp -f $lgop -h $laof $usenaivepairscore < infile > /dev/null 2>>"$progressfile" || exit 1 - mv hat2 hat2i - "$prefix/pairlocalalign" $localparam $addarg -C $numthreads $seqtype $model -g $lexp -f $lgop -Q $spfactor -h $laof -Y $usenaivepairscore < infile > /dev/null 2>>"$progressfile" || exit 1 - cat hat3.seed hat3 > hatx - mv hat2 hat2n - mv hatx hat3 - if [ $fragment -ne 0 ]; then - "$prefix/addsingle" $codonposopt $codonscoreopt -Q 100 $legacygapopt -d -O $outnum $addsinglearg $addarg $add2ndhalfarg -C $numthreads $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h $aof $param_fft $localparam $algopt $treealg < infile > /dev/null 2>>"$progressfile" || exit 1 - else - echo "Impossible" 1>&2 - exit 1 - fi - elif [ $distance = "hybrid" ]; then - "$prefix/pairlocalalign" $addarg -C $numthreads $seqtype $model -g $lexp -f $lgop -Q $spfactor -h $laof -Y < infile > /dev/null 2>>"$progressfile" || exit 1 - cat hat3.seed hat3 > hatx - mv hatx hat3 - "$prefix/disttbfast" -E 1 -s $unalignlevel $legacygapopt -W $tuplesize $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreads-$numthreadstb $memopt $weightopt $treeinopt $treeoutopt -T -y $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1 - if [ $fragment -ne 0 ]; then - "$prefix/addsingle" $codonposopt $codonscoreopt -Q 100 $legacygapopt -O $outnum $addsinglearg $addarg $add2ndhalfarg -C $numthreads $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h $aof $param_fft $localparam $algopt $treealg < infile > /dev/null 2>>"$progressfile" || exit 1 - else - "$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1 - fi -# elif [ $distance = "distonly" ]; then -# "$prefix/pairlocalalign" -C $numthreads $seqtype $model -g $pgexp -f $pggop -Q $spfactor -h $pgaof -t < infile > /dev/null 2>>"$progressfile" || exit 1 -# "$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1 - elif [ $distance = "parttree" ]; then - "$prefix/splittbfast" $legacygapopt $algopt $splitopt $partorderopt $parttreeoutopt $memopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof -p $partsize -s $groupsize $treealg $outnum -i infile > pre 2>>"$progressfile" || exit 1 - mv hat3.seed hat3 - elif [ $distance = "ktuplesmulti" ]; then -# "$prefix/dndpre" $model -M 1 $addarg -C $numthreads $seqtype $model -g $lexp -f $lgop -h $laof < infile > /dev/null 2>>"$progressfile" || exit 1 -# mv hat2 hat2i -# "$prefix/disttbfast" -E 1 -s $unalignlevel $legacygapopt -W $tuplesize $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreads-$numthreadstb $memopt $weightopt $treeinopt $treeoutopt -T -y $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $algopt $treealg $scoreoutarg < infile > /dev/null 2>>"$progressfile" || exit 1 -# mv hat2 hat2n - if [ $fragment -ne 0 ]; then - "$prefix/addsingle" $codonposopt $codonscoreopt -Q 100 $legacygapopt -d -W $tuplesize -O $outnum $addsinglearg $addarg $add2ndhalfarg -C $numthreads $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h $aof $param_fft $localparam $algopt $treealg < infile > /dev/null 2>>"$progressfile" || exit 1 -# "$prefix/addsingle" -Q 100 $legacygapopt -d -O $outnum $addsinglearg $addarg $add2ndhalfarg -C $numthreads $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h $aof $param_fft $localparam $algopt $treealg < infile > /dev/null 2>>"$progressfile" || exit 1 - else - echo "Impossible" 1>&2 - exit 1 - fi - else - if [ $fragment -ne 0 ]; then - "$prefix/addsingle" $codonposopt $codonscoreopt -Q 100 $legacygapopt -W $tuplesize -O $outnum $addsinglearg $addarg $add2ndhalfarg -C $numthreads $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -h $aof $param_fft $localparam $algopt $treealg < infile > /dev/null 2>>"$progressfile" || exit 1 - else - "$prefix/disttbfast" -q $npickup -E $cycledisttbfast -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg -W $tuplesize $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreads-$numthreadstb $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -g $gexp -f "-"$gop -Q $spfactor -h $aof $param_fft $algopt $treealg $scoreoutarg $anchoropt -x $maxanchorseparation $oneiterationopt < infile > pre 2>>"$progressfile" || exit 1 - mv hat3.seed hat3 - fi - fi - while [ $cycletbfast -gt 1 ] - do - if [ $distance = "parttree" ]; then - mv pre infile - "$prefix/splittbfast" $legacygapopt -Z $algopt $splitopt $partorderopt $parttreeoutopt $memopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof -p $partsize -s $groupsize $treealg $outnum -i infile > pre 2>>"$progressfile" || exit 1 - else - "$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $termgapopt $outnum -C $numthreadstb $rnaopt $weightopt $treeoutopt $distoutopt $memopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $localparam $algopt -J $treealg $scoreoutarg < pre > /dev/null 2>>"$progressfile" || exit 1 -# fragment>0 no baai, nanimoshinai -# seed youchuui!! - fi - cycletbfast=`expr $cycletbfast - 1` - done - if [ $iterate -gt 0 ]; then - if [ $distance = "ktuples" ]; then - "$prefix/dndpre" $seqtype $model -M 2 -C $numthreads < pre > /dev/null 2>>"$progressfile" || exit 1 - fi - "$prefix/dvtditr" -W $minimumweight $bunkatsuopt -E $fixthreshold -s $unalignlevel $legacygapopt $mergearg $outnum -C $numthreadsit -t $randomseed $rnaoptit $memopt $scorecalcopt $localparam -z 50 $seqtype $model -f "-"$gop -Q $spfactor -h $aof -I $iterate $weightopt $treeinopt $algoptit $treealg -p $parallelizationstrategy $scoreoutarg -K $nadd < pre > /dev/null 2>>"$progressfile" || exit 1 - fi - if [ $coreout -eq 1 ]; then - "$prefix/setcore" -w $corewin -i $corethr $coreext < pre > pre2 - mv pre2 pre - elif [ $anysymbol -eq 1 ]; then - "$prefix/restoreu" $add2ndhalfarg -a pre -i orig > restored || exit 1 - mv restored pre - fi - - - - - echo '' 1>>"$progressfile" - if [ $mccaskill -eq 1 ]; then - echo "RNA base pairing probaility was calculated by the McCaskill algorithm (1)" 1>>"$progressfile" - echo "implemented in Vienna RNA package (2) and MXSCARNA (3), and then" 1>>"$progressfile" - echo "incorporated in the iterative alignment process (4)." 1>>"$progressfile" - echo "(1) McCaskill, 1990, Biopolymers 29:1105-1119" 1>>"$progressfile" - echo "(2) Hofacker et al., 2002, J. Mol. Biol. 319:3724-3732" 1>>"$progressfile" - echo "(3) Tabei et al., 2008, BMC Bioinformatics 9:33" 1>>"$progressfile" - echo "(4) Katoh and Toh, 2008, BMC Bioinformatics 9:212" 1>>"$progressfile" - echo "" 1>>"$progressfile" - elif [ $contrafold -eq 1 ]; then - echo "RNA base pairing probaility was calculated by the CONTRAfold algorithm (1)" 1>>"$progressfile" - echo "and then incorporated in the iterative alignment process (4)." 1>>"$progressfile" - echo "(1) Do et al., 2006, Bioinformatics 22:e90-98" 1>>"$progressfile" - echo "(2) Katoh and Toh, 2008, BMC Bioinformatics 9:212" 1>>"$progressfile" - echo "" 1>>"$progressfile" - fi - if [ $pdblist != "/dev/null" -o $ownlist != "/dev/null" ]; then - echo "Input structures are decomposed into structural domains using" 1>>"$progressfile" - echo "Protein Domain Parser (Alexandrov & Shindyalov 2003)." 1>>"$progressfile" - echo "Domain pairs are aligned using the rash function in" 1>>"$progressfile" - echo "the ASH structural alignment package (Standley et al. 2007)." 1>>"$progressfile" - fi - if [ $pdblist != "/dev/null" ]; then - echo "Pre-computed alignments stored in " 1>>"$progressfile" - echo "DASH (http://sysimm.ifrec.osaka-u.ac.jp/dash/) are used. " 1>>"$progressfile" - fi - if [ $distance = "fasta" -o $partdist = "fasta" ]; then - echo "Pairwise alignments were computed by FASTA" 1>>"$progressfile" - echo "(Pearson & Lipman, 1988, PNAS 85:2444-2448)" 1>>"$progressfile" - fi - if [ $distance = "blast" ]; then - echo "Pairwise alignments were computed by BLAST" 1>>"$progressfile" - echo "(Altschul et al., 1997, NAR 25:3389-3402)" 1>>"$progressfile" - fi - if [ $distance = "last" -o $distance = "lastmulti" ]; then - echo "Pairwise alignments were computed by LAST" 1>>"$progressfile" - echo "http://last.cbrc.jp/" 1>>"$progressfile" - echo "Kielbasa, Wan, Sato, Horton, Frith 2011 Genome Res. 21:487" 1>>"$progressfile" - fi - if [ $distance = "scarna" ]; then - echo "Pairwise alignments were computed by MXSCARNA" 1>>"$progressfile" - echo "(Tabei et al., 2008, BMC Bioinformatics 9:33)." 1>>"$progressfile" - fi - if [ $distance = "dafs" ]; then - echo "Pairwise alignments were computed by DAFS" 1>>"$progressfile" - echo "(Sato et al., 2012,,,,)." 1>>"$progressfile" - fi - if [ $distance = "lara" -o $distance = "slara" ]; then - echo "Pairwise alignments were computed by LaRA" 1>>"$progressfile" - echo "(Bauer et al., 2007, BMC Bioinformatics 8:271)." 1>>"$progressfile" - fi - if [ $distance = "foldalignlocal" ]; then - echo "Pairwise alignments were computed by FOLDALIGN (local)" 1>>"$progressfile" - echo "(Havgaard et al., 2007, PLoS Computational Biology 3:e193)." 1>>"$progressfile" - fi - if [ $distance = "foldalignglobal" ]; then - echo "Pairwise alignments were computed by FOLDALIGN (global)" 1>>"$progressfile" - echo "(Havgaard et al., 2007, PLoS Computational Biology 3:e193)." 1>>"$progressfile" - fi -# printf "\n" 1>>"$progressfile" - echo 'Strategy:' 1>>"$progressfile" - printf ' '$strategy 1>>"$progressfile" - echo ' ('$performance')' 1>>"$progressfile" - echo ' '$explanation 1>>"$progressfile" - echo '' 1>>"$progressfile" - echo "If unsure which option to use, try 'mafft --auto input > output'." 1>>"$progressfile" - echo "For more information, see 'mafft --help', 'mafft --man' and the mafft page." 1>>"$progressfile" - echo "" 1>>"$progressfile" - echo "The default gap scoring scheme has been changed in version 7.110 (2013 Oct)." 1>>"$progressfile" - echo "It tends to insert more gaps into gap-rich regions than previous versions." 1>>"$progressfile" - echo "To disable this change, add the --leavegappyregion option." 1>>"$progressfile" -# echo "If long gaps are expected, try 'mafft --ep 0.0 --auto input > output'." 1>>"$progressfile" -# echo "If the possibility of long gaps can be excluded, add '--ep 0.123'." 1>>"$progressfile" - if [ $distance = "localgenaf" -o $distance = "globalgenaf" ]; then - echo "" 1>>"$progressfile" - if [ $oldgenafparam -eq 1 ]; then - echo "Obsolete parameters used for this calculation." 1>>"$progressfile" - echo "Also try the new parameters for E-INS-i, by not specifying --oldgenafpair." 1>>"$progressfile" - else - echo "Parameters for the E-INS-i option have been changed in version 7.243 (2015 Jun)." 1>>"$progressfile" - echo "To switch to the old parameters, use --oldgenafpair, instead of --genafpair." 1>>"$progressfile" - fi - fi - echo '' 1>>"$progressfile" - - - if [ $pdblist != "/dev/null" -o $ownlist != "/dev/null" ]; then -# cat dasherr >>"$progressfile" - echo '' >>"$progressfile" - fi - - popd > /dev/null - - if [ "$outputopt" != "-f -l -1" -o "$windows" = "yes" ]; then # Windows deha kaigyo code wo f2cl de modosu. -# ln -s "$TMPFILE/order" _order$$ # f2cl ga space ari filename ni taiou shiteinainode -# cp "$TMPFILE/order" _order$$ # ln -s no error wo sakeru - if [ "$outputfile" = "" ]; then - "$prefix/f2cl" -n $namelength $outputopt < "$TMPFILE/pre" 2>"/dev/null" || exit 1 - else - "$prefix/f2cl" -n $namelength $outputopt < "$TMPFILE/pre" > "$outputfile" 2>"/dev/null" || exit 1 - fi -# rm _order$$ - else - if [ "$outputfile" = "" ]; then - cat < "$TMPFILE/pre" || exit 1 - else - cat < "$TMPFILE/pre" > "$outputfile" || exit 1 - fi - fi - - if [ $treeout -eq 1 ]; then - cp "$TMPFILE/infile.tree" "$infilename.tree" - fi - - if [ -s "$TMPFILE/GuideTree" ]; then # --merge no toki dake - cp "$TMPFILE/GuideTree" . - fi - - if [ $distout -eq 1 ]; then - cp "$TMPFILE/hat2" "$infilename.hat2" - fi - - if [ $npickup -ne 0 ]; then - cp "$TMPFILE/notused" "$infilename.notused" - fi - - if [ -s "$TMPFILE/_deletemap" ]; then - if [ "$mapoutfile" = "/dev/null" ]; then - cp "$TMPFILE/_deletemap" "$addfile.map" - else - cp "$TMPFILE/_deletemap" "$mapoutfile" - fi - fi - - exit 0; -fi - -prog="awk" - -#tmpawk=`which nawk 2>/dev/null | awk '{print $1}'` -#if [ -x "$tmpawk" ]; then -# prog="$tmpawk" -#fi -# -#tmpawk=`which gawk 2>/dev/null | awk '{print $1}'` -#if [ -x "$tmpawk" ]; then -# prog="$tmpawk" -#fi -# 2017/May/12, Windows no gawk wo sakeru tame - -#echo "prog="$prog 1>&2 - -umask 077 -( -$prog ' -BEGIN { - prefix = ENVIRON["prefix"]; - version = ENVIRON["version"]; - myself = ENVIRON["myself"]; - pwd = ENVIRON["mafft_working_dir"]; # from mafft.bat on windows - if( pwd == "" ) pwd = ENVIRON["PWD"]; - while( 1 ) - { - options = "" - printf( "\n" ) > "/dev/tty"; - printf( "---------------------------------------------------------------------\n" ) > "/dev/tty"; - printf( "\n" ) > "/dev/tty"; - printf( " MAFFT %s\n", version ) > "/dev/tty"; - printf( "\n" ) > "/dev/tty"; -# printf( " Copyright (c) 2002- Kazutaka Katoh\n" ) > "/dev/tty"; - printf( " MBE 30:772-780 (2013), NAR 30:3059-3066 (2002)\n" ) > "/dev/tty"; - printf( " https://mafft.cbrc.jp/alignment/software/\n" ) > "/dev/tty"; - printf( "---------------------------------------------------------------------\n" ) > "/dev/tty"; - printf( "\n" ) > "/dev/tty"; - - while( 1 ) - { - printf( "\n" ) > "/dev/tty"; - printf( "Input file? (FASTA format; Folder=%s)\n@ ", pwd ) > "/dev/tty"; - res = getline < "/dev/tty"; - close( "/dev/tty" ) - if( res == 0 || NF == 0 ) - continue; - infile = sprintf( "%s", $0 ); - - res = getline < infile; - close( infile ); - if( res == -1 ) - { - printf( "%s: No such file.\n\n", infile ) > "/dev/tty"; - printf( "Filename extension (eg., .txt) must be typed, if any.\n\n" ) > "/dev/tty"; - } - else if( res == 0 ) - printf( "%s: Empty.\n", infile ) > "/dev/tty"; - else - { - printf( "OK. infile = %s\n\n", infile ) > "/dev/tty"; - break; - } - } - nseq = 0; - - while( 1 ) - { - printf( "\n" ) > "/dev/tty"; - printf( "Output file?\n" ) > "/dev/tty"; - printf( "@ " ) > "/dev/tty"; - res = getline < "/dev/tty"; - close( "/dev/tty" ); - if( res == 0 || NF == 0 ) - continue; - else - { - outfile = sprintf( "%s", $0 ); - printf( "OK. outfile = %s\n\n", outfile ) > "/dev/tty"; - break; - } - } - - while( 1 ) - { - outargs = ""; - printf( "\n" ) > "/dev/tty"; - printf( "Output format?\n" ) > "/dev/tty"; - printf( " 1. Clustal format / Sorted\n" ) > "/dev/tty"; - printf( " 2. Clustal format / Input order\n" ) > "/dev/tty"; - printf( " 3. Fasta format / Sorted\n" ) > "/dev/tty"; - printf( " 4. Fasta format / Input order\n" ) > "/dev/tty"; - printf( " 5. Phylip format / Sorted\n" ) > "/dev/tty"; - printf( " 6. Phylip format / Input order\n" ) > "/dev/tty"; - printf( "@ " ) > "/dev/tty"; - res = getline < "/dev/tty"; - close( "/dev/tty" ); -# printf( "res=%d, NF=%d\n", res, NF ); - - resnum = 0 + $1; -# printf( "resnum=%d\n", resnum ); - - if( resnum < 1 || 6 < resnum ) - continue; - else - { - if( resnum == 1 ) - outargs = "--clustalout --reorder"; - else if( resnum == 2 ) - outargs = "--clustalout --inputorder"; - else if( resnum == 3 ) - outargs = "--reorder"; - else if( resnum == 4 ) - outargs = "--inputorder"; - else if( resnum == 5 ) - outargs = "--phylipout --reorder"; - else if( resnum == 6 ) - outargs = "--phylipout --inputorder"; - else - continue; - printf( "OK. arguments = %s\n\n", outargs ) > "/dev/tty"; - break; - } - } - - while( 1 ) - { - arguments = ""; - printf( "\n" ) > "/dev/tty"; - printf( "Strategy?\n" ) > "/dev/tty"; - printf( " 1. --auto\n" ) > "/dev/tty"; - printf( " 2. FFT-NS-1 (fast)\n" ) > "/dev/tty"; - printf( " 3. FFT-NS-2 (default)\n" ) > "/dev/tty"; - printf( " 4. G-INS-i (accurate)\n" ) > "/dev/tty"; - printf( " 5. L-INS-i (accurate)\n" ) > "/dev/tty"; - printf( " 6. E-INS-i (accurate)\n" ) > "/dev/tty"; - printf( "@ " ) > "/dev/tty"; - res = getline < "/dev/tty"; - close( "/dev/tty" ); -# printf( "res=%d, NF=%d\n", res, NF ); - - resnum = 0 + $1; -# printf( "resnum=%d\n", resnum ); - - if( resnum < 1 || 6 < resnum ) - continue; - else - { - if( resnum == 1 ) - arguments = "--auto"; - else if( resnum == 2 ) - arguments = "--retree 1"; - else if( resnum == 3 ) - arguments = "--retree 2"; - else if( resnum == 4 ) - arguments = "--globalpair --maxiterate 16"; - else if( resnum == 5 ) - arguments = "--localpair --maxiterate 16"; - else if( resnum == 6 ) - arguments = "--genafpair --maxiterate 16"; - else - arguments = sprintf( "%s", $0 ); - printf( "OK. arguments = %s %s\n\n", arguments, outargs ) > "/dev/tty"; - break; - } - } - - - while( 1 ) - { - printf( "\n" ) > "/dev/tty"; - printf( "Additional arguments? (--ep # --op # --kappa # etc)\n" ) > "/dev/tty"; - printf( "@ " ) > "/dev/tty"; - res = getline < "/dev/tty"; - close( "/dev/tty" ); - if( res == 0 || NF == 0 ) - { - break; - } - else - { - addargs = sprintf( "%s", $0 ); - printf( "OK. arguments = %s %s %s\n\n", addargs, arguments, outargs ) > "/dev/tty"; - break; - } - } - - arguments = sprintf( "%s %s %s", addargs, arguments, outargs ); - - print "" - command = sprintf( "\"%s\" %s \"%s\" > \"%s\"", myself, arguments, infile, outfile ); - gsub( /\\/, "/", command ); - - - printf( "command=\n%s\n", command ) > "/dev/tty"; - - - while( 1 ) - { - go = 0; - printf( "Type Y or just enter to run this command.\n" ) > "/dev/tty"; - printf( "@ " ) > "/dev/tty"; - res = getline < "/dev/tty"; - close( "/dev/tty" ); - if( res == 0 ) - continue; - else if( NF == 0 || $0 ~ /^[Yy]/ ) - { - go=1; - break; - } - else - break; - } - if( go ) break; - printf( "\n" ) > "/dev/tty"; - printf( "\n" ) > "/dev/tty"; - } - system( command ); - command = sprintf( "more \"%s\"", outfile ); - system( command ); - printf( "Press Enter to exit." ) > "/dev/tty"; - res = getline < "/dev/tty"; -} -' -) -exit 0; diff --git a/aphylogeo/bin/mafft-win/usr/bin/mafft-homologs.rb b/aphylogeo/bin/mafft-win/usr/bin/mafft-homologs.rb deleted file mode 100644 index 3a62cc4d..00000000 --- a/aphylogeo/bin/mafft-win/usr/bin/mafft-homologs.rb +++ /dev/null @@ -1,505 +0,0 @@ -#!/usr/bin/env ruby - -localdb = "sp" -# database name from which homologues are collected -# by locally installed blast. Leave this if you do -# not use the '-l' option. - -mafftpath = "/usr/local/bin/mafft" -# path of mafft. "/usr/local/bin/mafft" -# if mafft is in your command path, "mafft" is ok. - -blastpath = "psiblast" -# path of blastall. -# if blastall is in your command path, "blastall" is ok. - -# mafft-homologs.rb v. 2.1 aligns sequences together with homologues -# automatically collected from SwissProt via NCBI BLAST. -# -# mafft > 5.58 is required -# -# Usage: -# mafft-homologs.rb [options] input > output -# Options: -# -a # the number of collected sequences (default: 50) -# -e # threshold value (default: 1e-10) -# -o "xxx" options for mafft -# (default: " --op 1.53 --ep 0.123 --maxiterate 1000") -# -l locally carries out blast searches instead of NCBI blast -# (requires locally installed blast and a database) -# -f outputs collected homologues also (default: off) -# -w entire sequences are subjected to BLAST search -# (default: well-aligned region only) - -#require 'getopts' -require 'optparse' -require 'tempfile' - -if ENV["MAFFT_BLAST"] && ENV["MAFFT_BLAST"] != "" then - blastpath = ENV["MAFFT_BLAST"] -end - -if ENV["MAFFT_HOMOLOGS_MAFFT"] && ENV["MAFFT_HOMOLOGS_MAFFT"] != "" then - mafftpath = ENV["MAFFT_HOMOLOGS_MAFFT"] -end - -# mktemp -GC.disable -temp_vf = Tempfile.new("_vf").path -temp_if = Tempfile.new("_if").path -temp_pf = Tempfile.new("_pf").path -temp_af = Tempfile.new("_af").path -temp_qf = Tempfile.new("_qf").path -temp_bf = Tempfile.new("_bf").path -temp_rid = Tempfile.new("_rid").path -temp_res = Tempfile.new("_res").path - - -system( mafftpath + " --help > #{temp_vf} 2>&1" ) -pfp = File.open( "#{temp_vf}", 'r' ) -while pfp.gets - break if $_ =~ /MAFFT v/ -end -pfp.close - -if( $_ ) then - mafftversion = $_.sub( /^\D*/, "" ).split(" ").slice(0).strip.to_s -else - mafftversion = "0" -end -if( mafftversion < "5.58" ) then - STDERR.puts "" - STDERR.puts "======================================================" - STDERR.puts "Install new mafft (v. >= 5.58)" - STDERR.puts "======================================================" - STDERR.puts "" - exit -end - -srand ( 0 ) - -def readfasta( fp, name, seq ) - nseq = 0 - tmpseq = "" - while fp.gets - if $_ =~ /^>/ then - name.push( $_.sub(/>/,"").strip ) - seq.push( tmpseq ) if nseq > 0 - nseq += 1 - tmpseq = "" - else - tmpseq += $_.strip - end - end - seq.push( tmpseq ) - return nseq -end - -nadd = 600 -num_alignments = 600 -num_threads_blast = 4 -eval = 1e-1 -local = 0 -fullout = 0 -entiresearch = 1 -corewin = 50 -corethr = 0.3 -#mafftopt = " --op 1.53 --ep 0.123 --localpair --maxiterate 1000 --reorder " -mafftopt = " --op 1.53 --ep 0.0 --globalpair --maxiterate 1000 --reorder " - - -#if getopts( "s", "f", "w", "l", "h", "e:", "a:", "o:", "c:", "d:" ) == nil || ARGV.length == 0 || $OPT_h then -# puts "Usage: #{$0} [-h -l -e# -a# -o\"[options for mafft]\"] input_file" -# exit -#end -params = ARGV.getopts( "sfwlhe:a:o:c:d:n:N:" ) - - -#if $OPT_c then -if params["c"] != nil then - corewin = params["c"].to_i -end - -#if $OPT_d then -#if params["d"] != nil then -# corethr = params["d"].to_f -#end -# -if params["d"] != nil then - localdb = params["d"].to_s -end - -if params["n"] != nil then - num_alignments = params["n"].to_s -end - -if params["N"] != nil then - num_threads_blast = params["N"].to_s -end - -#if $OPT_w -if params["w"] == true then - entiresearch = 1 -end - -#if $OPT_f -if params["f"] == true then - fullout = 1 -end - -#if $OPT_s -if params["s"] == true then - fullout = 0 -end - -#if $OPT_l -if params["l"] == true then - local = 1 -end - -#if $OPT_e then -if params["e"] != nil then -# eval = $OPT_e.to_f - eval = params["e"].to_f -end - -#if $OPT_a then -if params["a"] != nil then - nadd = params["a"].to_i -end - -#if $OPT_o then -if params["o"] != nil then - mafftopt += " " + params["o"] + " " -end - -infn = ARGV[0].to_s.strip - -system "cat " + infn + " > #{temp_if}" -ar = mafftopt.split(" ") -nar = ar.length -for i in 0..(nar-1) - if ar[i] == "--seed" then - system "cat #{ar[i+1]} >> #{temp_if}" - end -end - -if fullout == 0 then - mafftopt += " --excludehomologs " -end - -nseq = 0 -ifp = File.open( "#{temp_if}", 'r' ) - while ifp.gets - nseq += 1 if $_ =~ /^>/ - end -ifp.close - -if nseq >= 10000 then - STDERR.puts "The number of input sequences must be <10000." - exit -elsif nseq == 1 then - system( "cp #{temp_if}" + " #{temp_pf}" ) -else - STDERR.puts "Performing preliminary alignment .. " - if entiresearch == 1 then -# system( mafftpath + " --maxiterate 1000 --localpair #{temp_if} > #{temp_pf}" ) - system( mafftpath + " --maxiterate 0 --retree 2 #{temp_if} > #{temp_pf}" ) - else - system( mafftpath + " --maxiterate 1000 --localpair --core --coreext --corethr #{corethr.to_s} --corewin #{corewin.to_s} #{temp_if} > #{temp_pf}" ) - end -end - -pfp = File.open( "#{temp_pf}", 'r' ) -inname = [] -inseq = [] -slen = [] -act = [] -nin = 0 -nin = readfasta( pfp, inname, inseq ) -for i in 0..(nin-1) - slen.push( inseq[i].gsub(/-/,"").length ) - act.push( 1 ) -end -pfp.close - -pfp = File.open( "#{temp_if}", 'r' ) -orname = [] -orseq = [] -nin = 0 -nin = readfasta( pfp, orname, orseq ) -pfp.close - -allen = inseq[0].length -for i in 0..(nin-2) - for j in (i+1)..(nin-1) - next if act[i] == 0 - next if act[j] == 0 - pid = 0.0 - total = 0 - for a in 0..(allen-1) - next if inseq[i][a,1] == "-" || inseq[j][a,1] == "-" - total += 1 - pid += 1.0 if inseq[i][a,1] == inseq[j][a,1] - end - pid /= total -# puts "#{i.to_s}, #{j.to_s}, #{pid.to_s}" - if pid > 0.5 then - if slen[i] < slen[j] - act[i] = 0 - else - act[j] = 0 - end - end - end -end -#p act - - -afp = File.open( "#{temp_af}", 'w' ) - -STDERR.puts "Searching .. \n" -ids = [] -add = [] -sco = [] -nblast = 0 # ato de tsukau kamo -for i in 0..(nin-1) - singleids = [] - singleadd = [] - - inseq[i].gsub!(/-/,"") - afp.puts ">" + orname[i] - afp.puts orseq[i] - -# afp.puts ">" + inname[i] -# afp.puts inseq[i] - - STDERR.puts "Query (#{i+1}/#{nin})\n" + inname[i] - if act[i] == 0 then - STDERR.puts "Skip.\n\n" - next - end - - if local == 0 then - command = "lynx -source 'https://www.ncbi.nlm.nih.gov/blast/Blast.cgi?QUERY=" + inseq[i] + "&DATABASE=swissprot&HITLIST_SIZE=" + nadd.to_s + "&FILTER=L&EXPECT='" + eval.to_s + "'&FORMAT_TYPE=TEXT&PROGRAM=blastp&SERVICE=plain&NCBI_GI=on&PAGE=Proteins&CMD=Put' > #{temp_rid}" - system command - - ridp = File.open( "#{temp_rid}", 'r' ) - while ridp.gets - break if $_ =~ / RID = (.*)/ - end - ridp.close - rid = $1.strip - STDERR.puts "Submitted to NCBI. rid = " + rid - - STDERR.printf "Waiting " - while 1 - STDERR.printf "." - sleep 10 - command = "lynx -source 'https://www.ncbi.nlm.nih.gov/blast/Blast.cgi?RID=" + rid + "&DESCRIPTIONS=500&ALIGNMENTS=" + nadd.to_s + "&ALIGNMENT_TYPE=Pairwise&OVERVIEW=no&CMD=Get&FORMAT_TYPE=XML' > #{temp_res}" - system command - resp = File.open( "#{temp_res}", 'r' ) -# resp.gets -# if $_ =~ /WAITING/ then -# resp.close -# next -# end - while( resp.gets ) - break if $_ =~ /QBlastInfoBegin/ - end - resp.gets - if $_ =~ /WAITING/ then - resp.close - next - else - resp.close - break - end - end - else -# puts "Not supported" -# exit - qfp = File.open( "#{temp_qf}", 'w' ) - qfp.puts "> " - qfp.puts inseq[i] - qfp.close - command = blastpath + " -num_iterations 2 -num_threads #{num_threads_blast} -evalue #{eval} -num_alignments #{num_alignments} -outfmt 5 -query #{temp_qf} -db #{localdb} > #{temp_res}" - system command -# system "cp #{temp_res} _res" - end - STDERR.puts " Done.\n\n" - - resp = File.open( "#{temp_res}", 'r' ) - hitnum = 0 - lasteval = "nohit" - - while resp.gets - break if $_ =~ /2<\/Iteration_iter-num>/ - end - - if $_ == nil then - STDERR.puts "no hit" - else - while 1 - while resp.gets - break if $_ =~ /(.*)<\/Hit_id>/ || $_ =~ /()/ - end - id = $1 - break if $_ =~ // - # p id - - starthit = 9999999 - endhit = -1 - startquery = 9999999 - endquery = -1 - target = "" - score = 0.0 - - while line = resp.gets - if line =~ /(.*)<\/Hsp_hit-from>/ - starthitcand=$1.to_i - elsif line =~ /(.*)<\/Hsp_hit-to>/ - endhitcand=$1.to_i - elsif line =~ /(.*)<\/Hsp_query-from>/ - startquerycand=$1.to_i - elsif line =~ /(.*)<\/Hsp_query-to>/ - endquerycand=$1.to_i - elsif $_ =~ /(.*)<\/Hsp_hseq>/ - targetcand = $1.sub( /-/, "" ).sub( /U/, "X" ) - elsif line =~ /(.*)<\/Hsp_bit-score>/ - scorecand=$1.to_f - elsif line =~ /(.*)<\/Hsp_evalue>/ - evalcand=$1.to_s - elsif line =~ /<\/Hsp>/ - if endhit == -1 then - starthit = starthitcand - endhit= endhitcand - startquery = startquerycand - endquery= endquerycand - target = targetcand - score = scorecand - lasteval = evalcand - else - # if endhit <= endhitcand && endquery <= endquerycand then - if endhit <= starthitcand && endquery <= startquerycand then - endhit = endhitcand - endquery = endquerycand - target = target + "XX" + targetcand - score = score + scorecand - end - # if starthitcand <= starthit && startquerycand <= startquery then - if endhitcand <= starthit && endquerycand <= startquery then - starthit = starthitcand - startquery = startquerycand - target = targetcand + "XX" + target - score = score + scorecand - end - end - elsif line =~ /<\/Hit>/ - hitnum = hitnum + 1 - break; - end - end - - singleids.push( id ) - singleadd.push( target ) - - known = ids.index( id ) - if known != nil then - if sco[known] >= score then - next - else - ids.delete_at( known ) - add.delete_at( known ) - sco.delete_at( known ) - end - end - ids.push( id ) - sco.push( score ) - add.push( target ) - - end - resp.close - end - - n = singleids.length - outnum = 0 - - totalprob = 0 - prob = [] - for m in 0..(n-1) -# prob[m] = 1.0 / population[eclass[m]] - prob[m] = 1.0 - totalprob += prob[m] - end -# puts "" - for m in 0..(n-1) - prob[m] /= (totalprob) - prob[m] *= (nadd.to_f / nin.to_f) - prob[m] = 1 if prob[m] > 1 - end - - - for m in 0..(n-1) - if rand( 1000000 ).to_f/1000000 < prob[m] then -# STDERR.puts "hit in " + m.to_s - afp.puts ">_addedbymaffte_" + singleids[m] - afp.puts singleadd[m] - end - end -end -afp.close - -STDERR.puts "Aligning .. " -system( mafftpath + mafftopt + "#{temp_af} > #{temp_bf}" ) -STDERR.puts "done." - -bfp = File.open( "#{temp_bf}", 'r' ) -outseq = [] -outnam = [] -readfasta( bfp, outnam, outseq ) -bfp.close - -outseq2 = [] -outnam2 = [] - -len = outseq.length -for i in 0..(len-1) -# p outnam[i] - if fullout == 0 && outnam[i] =~ /_addedbymaffte_/ then - next - end - outseq2.push( outseq[i] ) - outnam2.push( outnam[i].sub( /_addedbymaffte_/, "_ho_" ) ) -end - -nout = outseq2.length -len = outseq[0].length -p = len -while p>0 - p -= 1 - allgap = 1 - for j in 0..(nout-1) - if outseq2[j][p,1] != "-" then - allgap = 0 - break - end - end - if allgap == 1 then - for j in 0..(nout-1) - outseq2[j][p,1] = "" - end - end -end -for i in 0..(nout-1) - puts ">" + outnam2[i] - puts outseq2[i].gsub( /.{1,60}/, "\\0\n" ) -end - - -system( "rm -rf #{temp_if} #{temp_vf} #{temp_af} #{temp_bf} #{temp_pf} #{temp_qf} #{temp_res} #{temp_rid}" ) -#system( "cp #{temp_if} #{temp_vf} #{temp_af} #{temp_bf} #{temp_pf} 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mode 100644 index a9c96825..00000000 --- a/aphylogeo/bin/mafft-win/usr/lib/mafft/mafft-homologs.1 +++ /dev/null @@ -1,131 +0,0 @@ -.\" Title: MAFFT-HOMOLOGS -.\" Author: Kazutaka Katoh -.\" Generator: DocBook XSL Stylesheets v1.72.0 -.\" Date: 2007-08-14 -.\" Manual: Mafft Manual -.\" Source: mafft-homologs 2.1 -.\" -.TH "MAFFT\-HOMOLOGS" "1" "2007\-06\-09" "mafft\-homologs 2.1" "Mafft Manual" -.\" disable hyphenation -.nh -.\" disable justification (adjust text to left margin only) -.ad l -.SH "NAME" -.RS 0 -mafft\-homologs \- aligns sequences together with homologues automatically collected from SwissProt via NCBI BLAST -.RE -.SH "SYNOPSIS" -.RS 0 -\fBmafft\-homologs\fR [\fBoptions\fR] \fIinput\fR [>\ \fIoutput\fR] -.RE -.SH "DESCRIPTION" -.RS 0 -The accuracy of an alignment of a few distantly related sequences is considerably improved when being aligned together with their close homologs. The reason for the improvement is probably the same as that for PSI\-BLAST. That is, the positions of highly conserved residues, those with many gaps and other additional information is brought by close homologs. According to Katoh et al. (2005), the improvement by adding close homologs is 10% or so, which is comparable to the improvement by incorporating structural information of a pair of sequences. Mafft\-homologs in a mafft server works like this: -.sp -.RS 4 -\h'-04' 1.\h'+02'Collect a number (50 by default) of close homologs (E=1e\-10 by default) of the input sequences. -.RE -.sp -.RS 4 -\h'-04' 2.\h'+02'Align the input sequences and homologs all together using the L\-INS\-i strategy. -.RE -.sp -.RS 4 -\h'-04' 3.\h'+02'Remove the homologs. -.RE -.RE -.SH "OPTIONS" -.RS 0 -.PP -\fB\-a\fR \fI\fIn\fR\fR -.RS 4 -The number of collected sequences (default: 50). -.RE -.PP -\fB\-e\fR \fI\fIn\fR\fR -.RS 4 -Threshold value (default: 1e\-10). -.RE -.PP -\fB\-o\fR \fI\fIxxx\fR\fR -.RS 4 -Options for mafft (default: " \-\-op 1.53 \-\-ep 0.123 \-\-maxiterate 1000 --localpair --reorder"). -.RE -.PP -\fB\-l\fR -.RS 4 -Locally carries out BLAST searches instead of NCBI BLAST (requires locally installed BLAST and a database). -.RE -.PP -\fB\-f\fR -.RS 4 -Outputs collected homologues also (default: off). -.RE -.PP -\fB\-w\fR -.RS 4 -entire sequences are subjected to BLAST search (default: well\-aligned region only) -.RE -.RE -.SH "REQUIREMENTS" -.RS 0 -.PP -MAFFT version > 5.58. -.PP -Either of -.RS 4 -.PP -lynx (when remote BLAST server is used) -.PP -BLAST and a protein sequence database (when local BLAST is used) -.RE -.RE -.SH "REFERENCES" -.RS 0 -.PP -Katoh, Kuma, Toh and Miyata (Nucleic Acids Res. 33:511\-518, 2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment. -.RE -.SH "SEE ALSO" -.RS 0 -.PP -\fBmafft\fR(1) -.RE -.SH "AUTHORS" -.RS 0 -.PP -\fBKazutaka Katoh\fR <\&katoh_at_bioreg.kyushu\-u.ac.jp.\&> -.sp -1n -.IP "" 4 -Wrote Mafft. -.PP -\fBCharles Plessy\fR <\&charles\-debian\-nospam@plessy.org\&> -.sp -1n -.IP "" 4 -Wrote this manpage in DocBook XML for the Debian distribution, using Mafft's homepage as a template. -.RE -.SH "COPYRIGHT" -.RS 0 -Copyright \(co 2002\-2007 Kazutaka Katoh (mafft) -.br -Copyright \(co 2007 Charles Plessy (this manpage) -.br -.PP -Mafft and its manpage are offered under the following conditions: -.PP -Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: -.sp -.RS 4 -\h'-04' 1.\h'+02'Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. -.RE -.sp -.RS 4 -\h'-04' 2.\h'+02'Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. -.RE -.sp -.RS 4 -\h'-04' 3.\h'+02'The name of the author may not be used to endorse or promote products derived from this software without specific prior written permission. -.RE -.PP -THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -.br -.RE diff --git a/aphylogeo/bin/mafft-win/usr/lib/mafft/mafft-profile.exe b/aphylogeo/bin/mafft-win/usr/lib/mafft/mafft-profile.exe deleted file mode 100644 index 4436c9db..00000000 Binary files a/aphylogeo/bin/mafft-win/usr/lib/mafft/mafft-profile.exe and /dev/null differ diff --git a/aphylogeo/bin/mafft-win/usr/lib/mafft/mafft.1 b/aphylogeo/bin/mafft-win/usr/lib/mafft/mafft.1 deleted file mode 100644 index b5344c57..00000000 --- a/aphylogeo/bin/mafft-win/usr/lib/mafft/mafft.1 +++ /dev/null @@ -1,479 +0,0 @@ -.\" Title: MAFFT -.\" Author: Kazutaka Katoh -.\" Generator: DocBook XSL Stylesheets v1.72.0 -.\" Date: 2007-08-14 -.\" Manual: Mafft Manual -.\" Source: mafft 6.240 -.\" -.TH "MAFFT" "1" "2007\-06\-09" "mafft 6.240" "Mafft Manual" -.\" disable hyphenation -.nh -.\" disable justification (adjust text to left margin only) -.ad l -.SH "THIS MANUAL IS FOR V6.2XX (2007)" -Recent versions (v7.1xx; 2013 Jan.) have more features than those described below. -See also the tips page at -http://mafft.cbrc.jp/alignment/software/tips0.html -.SH "NAME" -.RS 0 -.sp -mafft \- Multiple alignment program for amino acid or nucleotide sequences -.RE -.SH "SYNOPSIS" -.RS 0 -.HP 6 -\fBmafft\fR [\fBoptions\fR] \fIinput\fR [>\ \fIoutput\fR] -.HP 6 -\fBlinsi\fR \fIinput\fR [>\ \fIoutput\fR] -.HP 6 -\fBginsi\fR \fIinput\fR [>\ \fIoutput\fR] -.HP 6 -\fBeinsi\fR \fIinput\fR [>\ \fIoutput\fR] -.HP 7 -\fBfftnsi\fR \fIinput\fR [>\ \fIoutput\fR] -.HP 6 -\fBfftns\fR \fIinput\fR [>\ \fIoutput\fR] -.HP 5 -\fBnwns\fR \fIinput\fR [>\ \fIoutput\fR] -.HP 6 -\fBnwnsi\fR \fIinput\fR [>\ \fIoutput\fR] -.HP 14 -\fBmafft\-profile\fR \fIgroup1\fR \fIgroup2\fR [>\ \fIoutput\fR] -.HP -.sp -\fIinput\fR, \fIgroup1\fR and \fIgroup2\fR must be in FASTA format. -.RE -.SH "DESCRIPTION" -.RS 0 -\fBMAFFT\fR is a multiple sequence alignment program for unix\-like operating systems. It offers a range of multiple alignment methods. -.SS "Accuracy\-oriented methods:" -.sp -.RS 4 -\h'-04'\(bu\h'+03'L\-INS\-i (probably most accurate; recommended for <200 sequences; iterative refinement method incorporating local pairwise alignment information): -.HP 6 -\fBmafft\fR \fB\-\-localpair\fR \fB\-\-maxiterate\fR\ \fI1000\fR \fIinput\fR [>\ \fIoutput\fR] -.HP 6 -\fBlinsi\fR \fIinput\fR [>\ \fIoutput\fR] -.RE -.sp -.RS 4 -\h'-04'\(bu\h'+03'G\-INS\-i (suitable for sequences of similar lengths; recommended for <200 sequences; iterative refinement method incorporating global pairwise alignment information): -.HP 6 -\fBmafft\fR \fB\-\-globalpair\fR \fB\-\-maxiterate\fR\ \fI1000\fR \fIinput\fR [>\ \fIoutput\fR] -.HP 6 -\fBginsi\fR \fIinput\fR [>\ \fIoutput\fR] -.RE -.sp -.RS 4 -\h'-04'\(bu\h'+03'E\-INS\-i (suitable for sequences containing large unalignable regions; recommended for <200 sequences): -.HP 6 -\fBmafft\fR \fB\-\-ep\fR\ \fI0\fR \fB\-\-genafpair\fR \fB\-\-maxiterate\fR\ \fI1000\fR \fIinput\fR [>\ \fIoutput\fR] -.HP 6 -\fBeinsi\fR \fIinput\fR [>\ \fIoutput\fR] -.br - -For E\-INS\-i, the -\fB\-\-ep\fR -\fI0\fR -option is recommended to allow large gaps. -.RE -.SS "Speed\-oriented methods:" -.sp -.RS 4 -\h'-04'\(bu\h'+03'FFT\-NS\-i (iterative refinement method; two cycles only): -.HP 6 -\fBmafft\fR \fB\-\-retree\fR\ \fI2\fR \fB\-\-maxiterate\fR\ \fI2\fR \fIinput\fR [>\ \fIoutput\fR] -.HP 7 -\fBfftnsi\fR \fIinput\fR [>\ \fIoutput\fR] -.RE -.sp -.RS 4 -\h'-04'\(bu\h'+03'FFT\-NS\-i (iterative refinement method; max. 1000 iterations): -.HP 6 -\fBmafft\fR \fB\-\-retree\fR\ \fI2\fR \fB\-\-maxiterate\fR\ \fI1000\fR \fIinput\fR [>\ \fIoutput\fR] -.RE -.sp -.RS 4 -\h'-04'\(bu\h'+03'FFT\-NS\-2 (fast; progressive method): -.HP 6 -\fBmafft\fR \fB\-\-retree\fR\ \fI2\fR \fB\-\-maxiterate\fR\ \fI0\fR \fIinput\fR [>\ \fIoutput\fR] -.HP 6 -\fBfftns\fR \fIinput\fR [>\ \fIoutput\fR] -.RE -.sp -.RS 4 -\h'-04'\(bu\h'+03'FFT\-NS\-1 (very fast; recommended for >2000 sequences; progressive method with a rough guide tree): -.HP 6 -\fBmafft\fR \fB\-\-retree\fR\ \fI1\fR \fB\-\-maxiterate\fR\ \fI0\fR \fIinput\fR [>\ \fIoutput\fR] -.RE -.sp -.RS 4 -\h'-04'\(bu\h'+03'NW\-NS\-i (iterative refinement method without FFT approximation; two cycles only): -.HP 6 -\fBmafft\fR \fB\-\-retree\fR\ \fI2\fR \fB\-\-maxiterate\fR\ \fI2\fR \fB\-\-nofft\fR\ \fIinput\fR [>\ \fIoutput\fR] -.HP 7 -\fBnwnsi\fR \fIinput\fR [>\ \fIoutput\fR] -.RE -.sp -.RS 4 -\h'-04'\(bu\h'+03'NW\-NS\-2 (fast; progressive method without the FFT approximation): -.HP 6 -\fBmafft\fR \fB\-\-retree\fR\ \fI2\fR \fB\-\-maxiterate\fR\ \fI0\fR \fB\-\-nofft\fR\ \fIinput\fR [>\ \fIoutput\fR] -.HP 6 -\fBnwns\fR \fIinput\fR [>\ \fIoutput\fR] -.RE -.sp -.RS 4 -\h'-04'\(bu\h'+03'NW\-NS\-PartTree\-1 (recommended for ~10,000 to ~50,000 sequences; progressive method with the PartTree algorithm): -.HP 6 -\fBmafft\fR \fB\-\-retree\fR\ \fI1\fR \fB\-\-maxiterate\fR\ \fI0\fR \fB\-\-nofft\fR\ \fB\-\-parttree\fR \fIinput\fR [>\ \fIoutput\fR] -.RE -.SS "Group\-to\-group alignments" -.HP 6 -.RS 4 -\fBmafft\-profile\fR \fIgroup1\fR \fIgroup2\fR [>\ \fIoutput\fR] -.sp -or: -.sp -\fBmafft\fR \fB\-\-maxiterate\fR\ \fI1000\fR \fB\-\-seed\fR\ \fIgroup1\fR \fB\-\-seed\fR\ \fIgroup2\fR /dev/null [>\ \fIoutput\fR] -.RE -.RE -.RE -.SH "OPTIONS" -.SS "Algorithm" -.RS 0 -.PP -\fB\-\-auto\fR -.RS 4 -Automatically selects an appropriate strategy from L\-INS\-i, FFT\-NS\-i and FFT\-NS\-2, according to data -size. Default: off (always FFT\-NS\-2) -.RE -.PP -\fB\-\-6merpair\fR -.RS 4 -Distance is calculated based on the number of shared 6mers. Default: on -.RE -.PP -\fB\-\-globalpair\fR -.RS 4 -All pairwise alignments are computed with the Needleman\-Wunsch -algorithm. More accurate but slower -than \-\-6merpair. Suitable for a set of -globally alignable sequences. Applicable to -up to ~200 sequences. A combination with \-\-maxiterate 1000 is recommended (G\-INS\-i). Default: off (6mer distance is used) -.RE -.PP -\fB\-\-localpair\fR -.RS 4 -All pairwise alignments are computed with the Smith\-Waterman -algorithm. More accurate but slower -than \-\-6merpair. Suitable for a set of -locally alignable sequences. Applicable to -up to ~200 sequences. A combination with \-\-maxiterate 1000 is recommended (L\-INS\-i). Default: off (6mer distance is used) -.RE -.PP -\fB\-\-genafpair\fR -.RS 4 -All pairwise alignments are computed with a local -algorithm with the generalized affine gap cost -(Altschul 1998). More accurate but slower -than \-\-6merpair. Suitable when large internal gaps -are expected. Applicable to -up to ~200 sequences. A combination with \-\-maxiterate 1000 is recommended (E\-INS\-i). Default: off (6mer distance is used) -.RE -.\".PP -.\"\fB\-\-fastswpair\fR -.\".RS 4 -.\"Distance is calculated based on a FASTA alignment. -.\"FASTA is required. Default: off (6mer distance is used) -.\".RE -.PP -\fB\-\-fastapair\fR -.RS 4 -All pairwise alignments are computed with FASTA (Pearson and Lipman 1988). -FASTA is required. Default: off (6mer distance is used) -.RE -.\".PP -.\"\fB\-\-blastpair\fR -.\".RS 4 -.\"Distance is calculated based on a BLAST alignment. BLAST is -.\"required. Default: off (6mer distance is used) -.\".RE -.PP -\fB\-\-weighti\fR \fInumber\fR -.RS 4 -Weighting factor for the consistency term calculated from pairwise alignments. Valid when -either of \-\-globalpair, \-\-localpair, \-\-genafpair, \-\-fastapair or -\-\-blastpair is selected. Default: 2.7 -.RE -.PP -\fB\-\-retree\fR \fInumber\fR -.RS 4 -Guide tree is built \fInumber\fR times in the -progressive stage. Valid with 6mer distance. Default: 2 -.RE -.PP -\fB\-\-maxiterate\fR \fInumber\fR -.RS 4 -\fInumber\fR cycles of iterative refinement are performed. Default: 0 -.RE -.PP -\fB\-\-fft\fR -.RS 4 -Use FFT approximation in group\-to\-group alignment. Default: on -.RE -.PP -\fB\-\-nofft\fR -.RS 4 -Do not use FFT approximation in group\-to\-group alignment. Default: off -.RE -.PP -\fB\-\-noscore\fR -.RS 4 -Alignment score is not checked in the iterative refinement stage. Default: off (score is checked) -.RE -.PP -\fB\-\-memsave\fR -.RS 4 -Use the Myers\-Miller (1988) algorithm. Default: automatically turned on when the alignment length exceeds 10,000 (aa/nt). -.RE -.PP -\fB\-\-parttree\fR -.RS 4 -Use a fast tree\-building method (PartTree, Katoh and Toh 2007) with -the 6mer distance. Recommended for a large number (> ~10,000) -of sequences are input. Default: off -.RE -.PP -\fB\-\-dpparttree\fR -.RS 4 -The PartTree algorithm is used with distances based on DP. Slightly -more accurate and slower than \-\-parttree. Recommended for a large -number (> ~10,000) of sequences are input. Default: off -.RE -.PP -\fB\-\-fastaparttree\fR -.RS 4 -The PartTree algorithm is used with distances based on FASTA. Slightly more accurate and slower than \-\-parttree. Recommended for a large number (> ~10,000) of sequences are input. FASTA is required. Default: off -.RE -.PP -\fB\-\-partsize\fR \fInumber\fR -.RS 4 -The number of partitions in the PartTree algorithm. Default: 50 -.RE -.PP -\fB\-\-groupsize\fR \fInumber\fR -.RS 4 -Do not make alignment larger than \fInumber\fR sequences. Valid only with the \-\-*parttree options. Default: the number of input sequences -.RE -.RE -.SS "Parameter" -.RS 0 -.PP -\fB\-\-op\fR \fInumber\fR -.RS 4 -Gap opening penalty at group\-to\-group alignment. Default: 1.53 -.RE -.PP -\fB\-\-ep\fR \fInumber\fR -.RS 4 -Offset value, which works like gap extension penalty, for -group\-to\-group alignment. Default: 0.123 -.RE -.PP -\fB\-\-lop\fR \fInumber\fR -.RS 4 -Gap opening penalty at local pairwise -alignment. Valid when -the \-\-localpair or \-\-genafpair option is selected. Default: \-2.00 -.RE -.PP -\fB\-\-lep\fR \fInumber\fR -.RS 4 -Offset value at local pairwise alignment. Valid when -the \-\-localpair or \-\-genafpair option is selected. Default: 0.1 -.RE -.PP -\fB\-\-lexp\fR \fInumber\fR -.RS 4 -Gap extension penalty at local pairwise alignment. Valid when -the \-\-localpair or \-\-genafpair option is selected. Default: \-0.1 -.RE -.PP -\fB\-\-LOP\fR \fInumber\fR -.RS 4 -Gap opening penalty to skip the alignment. Valid when the -\-\-genafpair option is selected. Default: \-6.00 -.RE -.PP -\fB\-\-LEXP\fR \fInumber\fR -.RS 4 -Gap extension penalty to skip the alignment. Valid when the -\-\-genafpair option is selected. Default: 0.00 -.RE -.PP -\fB\-\-bl\fR \fInumber\fR -.RS 4 -BLOSUM \fInumber\fR matrix (Henikoff and Henikoff 1992) is used. \fInumber\fR=30, 45, 62 or 80. Default: 62 -.RE -.PP -\fB\-\-jtt\fR \fInumber\fR -.RS 4 -JTT PAM \fInumber\fR (Jones et al. 1992) matrix is used. \fInumber\fR>0. Default: BLOSUM62 -.RE -.PP -\fB\-\-tm\fR \fInumber\fR -.RS 4 -Transmembrane PAM \fInumber\fR (Jones et al. 1994) matrix is used. \fInumber\fR>0. Default: BLOSUM62 -.RE -.PP -\fB\-\-aamatrix\fR \fImatrixfile\fR -.RS 4 -Use a user\-defined AA scoring matrix. The format of \fImatrixfile\fR is -the same to that of BLAST. Ignored when nucleotide sequences are input. Default: BLOSUM62 -.RE -.PP -\fB\-\-fmodel\fR -.RS 4 -Incorporate the AA/nuc composition information into -the scoring matrix. Default: off -.RE -.RE -.SS "Output" -.RS 0 -.PP -\fB\-\-clustalout\fR -.RS 4 -Output format: clustal format. Default: off (fasta format) -.RE -.PP -\fB\-\-inputorder\fR -.RS 4 -Output order: same as input. Default: on -.RE -.PP -\fB\-\-reorder\fR -.RS 4 -Output order: aligned. Default: off (inputorder) -.RE -.PP -\fB\-\-treeout\fR -.RS 4 -Guide tree is output to the \fIinput\fR.tree file. Default: off -.RE -.PP -\fB\-\-quiet\fR -.RS 4 -Do not report progress. Default: off -.RE -.RE -.SS "Input" -.RS 0 -.PP -\fB\-\-nuc\fR -.RS 4 -Assume the sequences are nucleotide. Default: auto -.RE -.PP -\fB\-\-amino\fR -.RS 4 -Assume the sequences are amino acid. Default: auto -.RE -.PP -\fB\-\-seed\fR \fIalignment1\fR [\fB--seed\fR \fIalignment2\fR \fB--seed\fR \fIalignment3\fR ...] -.RS 4 -Seed alignments given in \fIalignment_n\fR (fasta format) are aligned with -sequences in \fIinput\fR. The alignment within every seed is preserved. -.RE -.RE -.SH "FILES" -.RS 0 -.PP -Mafft stores the input sequences and other files in a temporary directory, which by default is located in -\fI/tmp\fR. -.RE -.SH "ENVIONMENT" -.RS 0 -.PP -\fBMAFFT_BINARIES\fR -.RS 4 -Indicates the location of the binary files used by mafft. By default, they are searched in -\fI/usr/local/lib/mafft\fR, but on Debian systems, they are searched in -\fI/usr/lib/mafft\fR. -.RE -.PP -\fBFASTA_4_MAFFT\fR -.RS 4 -This variable can be set to indicate to mafft the location to the fasta34 program if it is not in the PATH. -.RE -.RE -.SH "SEE ALSO" -.RS 0 -.PP - -\fBmafft\-homologs\fR(1) -.RE -.SH "REFERENCES" -.RS 0 -.SS "In English" -.sp -.RS 4 -\h'-04'\(bu\h'+03'Katoh and Toh (Bioinformatics 23:372\-374, 2007) PartTree: an algorithm to build an approximate tree from a large number of unaligned sequences (describes the PartTree algorithm). -.RE -.sp -.RS 4 -\h'-04'\(bu\h'+03'Katoh, Kuma, Toh and Miyata (Nucleic Acids Res. 33:511\-518, 2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment (describes [ancestral versions of] the G\-INS\-i, L\-INS\-i and E\-INS\-i strategies) -.RE -.sp -.RS 4 -\h'-04'\(bu\h'+03'Katoh, Misawa, Kuma and Miyata (Nucleic Acids Res. 30:3059\-3066, 2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform (describes the FFT\-NS\-1, FFT\-NS\-2 and FFT\-NS\-i strategies) -.RE -.SS "In Japanese" -.sp -.RS 4 -\h'-04'\(bu\h'+03'Katoh and Misawa (Seibutsubutsuri 46:312\-317, 2006) Multiple Sequence Alignments: the Next Generation -.RE -.sp -.RS 4 -\h'-04'\(bu\h'+03'Katoh and Kuma (Kagaku to Seibutsu 44:102\-108, 2006) Jissen\-teki Multiple Alignment -.RE -.RE -.SH "AUTHORS" -.RS 0 -.PP -\fBKazutaka Katoh\fR <\&kazutaka.katoh_at_aist.go.jp\&> -.sp -1n -.IP "" 4 -Wrote Mafft. -.PP -\fBCharles Plessy\fR <\&charles\-debian\-nospam_at_plessy.org\&> -.sp -1n -.IP "" 4 -Wrote this manpage in DocBook XML for the Debian distribution, using Mafft's homepage as a template. -.RE -.SH "COPYRIGHT" -.RS 0 -Copyright \(co 2002\-2007 Kazutaka Katoh (mafft) -.br -Copyright \(co 2007 Charles Plessy (this manpage) -.br -.PP -Mafft and its manpage are offered under the following conditions: -.PP -Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: -.sp -.RS 4 -\h'-04' 1.\h'+02'Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. -.RE -.sp -.RS 4 -\h'-04' 2.\h'+02'Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. -.RE -.sp -.RS 4 -\h'-04' 3.\h'+02'The name of the author may not be used to endorse or promote products derived from this software without specific prior written permission. -.RE -.PP -THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -.br -.RE diff --git a/aphylogeo/bin/mafft-win/usr/lib/mafft/mafftash_premafft.pl b/aphylogeo/bin/mafft-win/usr/lib/mafft/mafftash_premafft.pl deleted file mode 100644 index 6dc3b9c4..00000000 --- a/aphylogeo/bin/mafft-win/usr/lib/mafft/mafftash_premafft.pl +++ /dev/null @@ -1,464 +0,0 @@ -#!/usr/bin/perl - -##################################################################### -# Author: KM Amada (kmamada@ifrec.osaka-u.ac.jp) -# -# Ver. Date Changelog -##################################################################### -# 1.0 07.26.13 Initial release -# 2.0 09.03.13 Added extensive warnings and error messages -# 3.0 10.28.13 Fix for retrieving large files. Added STDERR logs -# 3.1 11.08.13 Added LWP failsafe. Made hat3 not a required output -# 3.2 12.08.14 Removed 5-char restriction for own structure files -# -##################################################################### - -use strict; -use Getopt::Long; -use File::Path qw(make_path remove_tree); -use LWP::Simple; -use LWP::UserAgent; - -# to prevent error 'Header line too long (limit is 8192)' [v3.1] -use LWP::Protocol::http; -push(@LWP::Protocol::http::EXTRA_SOCK_OPTS, MaxLineLength => 0); - - - -my $BASEURL = "http://sysimm.ifrec.osaka-u.ac.jp/MAFFTash/REST/service.cgi/premafft"; - -my ( $WORKDIR, $PDBLIST, $OWNLIST, $HAT3FILE, $INSTRFILE ); - -GetOptions -( - 'd=s' => \$WORKDIR, - 'p=s' => \$PDBLIST, - 'o=s' => \$OWNLIST, - 'h=s' => \$HAT3FILE, - 'i=s' => \$INSTRFILE, -); - -print STDERR "[MAFFTash-premafft]\n"; - -# set temp directory -my $TMP = "/tmp/mapremafft$$"; -make_path($TMP) unless -d $TMP; - - - -###### -# validation -&help("Required parameter : atleast one of either '-p' or '-o'") unless ( defined $PDBLIST || defined $OWNLIST); -&help("Required parameter : '-d'") if defined $OWNLIST && ! defined $WORKDIR; - -$HAT3FILE = "hat3" unless defined $HAT3FILE; -$INSTRFILE = "instr" unless defined $INSTRFILE; -chop $WORKDIR if defined $WORKDIR && $WORKDIR =~ m/\/$/g; - - -###### -# prepare inputs -print STDERR "Preparing inputs for service request...\n"; - -my @files = (); -push(@files, "strweight" => "0.5"); -push(@files, "premafft" => "1"); - - -# pdb entries -if ( defined $PDBLIST ) -{ - print STDERR "PDB List defined!\n"; - &bail("Error: Input file $PDBLIST does not exists!") unless -e $PDBLIST; - my $listfile = "$TMP/pdblist.inp"; - - - open(INPF,"<$PDBLIST") or &bail("Error: Cannot open file $PDBLIST for reading!"); - open(OUTF,">$listfile") or &bail("Error: Cannot open temporary file $listfile for writing!"); - - while() - { - chomp; - if ( /^(\w{5})$/ ) - { - print OUTF ">PDBID\n$1\n"; - } - } - - close OUTF; - close INPF; - - push(@files, "inputfile" => ["$listfile"]); -} - - - -# upload own structures -my %ownids = (); - -if ( defined $OWNLIST ) -{ - print STDERR "OWN List defined!\n"; - &bail("Error: Input file $OWNLIST does not exists!") unless -e $OWNLIST; - - - open(OWNINPF,"<$OWNLIST") or &bail("Error: Cannot open file $OWNLIST for reading!"); - - while() - { - chomp; - - if ( /^(\S+)$/ ) - { - my $fileref = "$WORKDIR/$1.pdb"; - - unless (-e $fileref) - { - close OWNINPF; - &bail("Error: File $fileref does not exists!"); - } - - push(@files, "inputownfile[]" => ["$fileref"]); - $ownids{$1} = 1; - } - } - - close OWNINPF; -} - - - -###### -# start rest service -print STDERR "Sending service request...\n"; - -my $browser = LWP::UserAgent->new; -$browser->timeout(0); - - -# post: running a mafftash job -my $postResponse = $browser->post( $BASEURL, \@files, 'Content_Type' => 'form-data' ); -&bail(sprintf("[%d] %s\n", $postResponse->code, &parseError($postResponse->content))) unless($postResponse->is_success); - - -# get response from post request -my ($status, $mafftashid) = &parseResponse($postResponse->content); - - - -my $MAXTRIES = 3; -my $STIMER = 4; -my $longtimer = 0; - -print STDERR "Request sent! Waiting for response...[$mafftashid]\n"; - - -# wait for results until it becomes available -while(1) -{ - $longtimer = $longtimer <= ($STIMER*3) ? $longtimer+$STIMER : $STIMER; - sleep $longtimer; - - - # get: get results for mafftash job - my $getResponse = $browser->get("$BASEURL/$mafftashid"); - - if ( $getResponse->is_success ) - { - - # get response from get request - ($status, $mafftashid) = &parseResponse($getResponse->content); - next unless ( $status eq "done" ); - - - # if job is finished and ready - print STDERR "Results found!\n"; - my $csfile = "$TMP/checksum.tar.gz"; - my $try1 = 1; - - - while(1) - { - print STDERR "Fetching Results... [Trial $try1]\n"; - - if ( is_success(getstore("$BASEURL/getmdlist/$mafftashid", $csfile)) && -e $csfile && -s $csfile ) - { - # get response from get request - my $checklist = &extractchecksum($csfile); - &bail("Error retrieving list of compressed files!") unless ( scalar %$checklist > 0 ); - - - foreach my $id ( keys %$checklist ) - { - my $checkfile = "$TMP/$id"; - my $checkid = $checklist->{$id}; - my $try2 = 1; - - while(1) - { - unlink $checkfile if -e $checkfile; - - if ( is_success(getstore("$BASEURL/get/$mafftashid/$id", $checkfile)) && -e $checkfile && -s $checkfile ) - { - my $hashid = &getchecksum($checkfile); - #print STDERR "[hashid]$hashid [checkid]$checkid\n"; - - if ($hashid ne "" && $hashid ne $checkid ) - { - unlink $checkfile if -e $checkfile; - &bail("Error retrieving compressed file from server! [Checksum Failed]") if $try2 >= $MAXTRIES; - $try2++; - sleep $STIMER; - } - else - { - last; - } - } - else - { - &bail("Error retrieving compressed file from server!") if $try2 >= $MAXTRIES; - $try2++; - sleep $STIMER; - } - } - } - - last; - } - else - { - &bail("Error retrieving list of compressed files from server!") if $try1 >= $MAXTRIES; - $try1++; - sleep $STIMER; - } - } - - last; - - } - else - { - &bail(sprintf("[%d] %s\n", $getResponse->code, &parseError($getResponse->content))); - } - -} - - -# make sure outputs were generated -# decompress -print STDERR "Assembling final results...\n"; - -&backticks("cat $TMP/archive.tar.gz* | tar -zxf - -C $TMP/"); -&backticks("mv -f $TMP/instr $INSTRFILE") if -e "$TMP/instr"; -&backticks("mv -f $TMP/hat3 $HAT3FILE") if -e "$TMP/hat3"; - -# sometimes no hat3 file is generated [v3.1] -#&bail("Error: Output file $HAT3FILE not found!") unless -e $HAT3FILE; -&bail("Error: Output file $INSTRFILE not found!") unless -e $INSTRFILE; - - -# warn if some ownids were ommitted -if ( scalar keys(%ownids) > 0 ) -{ - my %instrids = (); - - open(INSTRF,"<$INSTRFILE") or &bail("Error: Cannot open file $INSTRFILE for reading!"); - - while() - { - chomp; - - if ( /^>\d+_(\S+)$/ ) - { - $instrids{$1} = 1; - } - } - - close INSTRF; - - foreach my $id ( keys %ownids ) - { - warn "Warning: Own structure $id was excluded from instr/hat3.\n" unless $instrids{$id}; - } - -} - - - -&cleanup(); - - - -#################### -#################### - - - -sub parseResponse -{ - my $response = shift; - - #"status":"wait","mafftashid":"Ma8211432R" - - my $status = ""; - my $mafftashid = ""; - - if ( $response =~ /^([^\s:]+):([^\s:]+)$/ ) - { - $mafftashid = $1; - $status = $2; - } - - return ($status, $mafftashid); - -} - - -sub extractchecksum -{ - my $infile = shift; - my %dataset = (); - - open CSUM, "tar -zxf $infile -O|" or return \%dataset; - - while() - { - chomp; - if ( /^(\S+)\s+(\S+)$/ ) - { - $dataset{$2} = $1; - } - - } - - close CSUM; - - return \%dataset; - -} - - -sub parseError -{ - my $response = shift; - - #"error":"Invalid number of inputs found." - my $errorstr = ( $response =~ /\"error\"\s*:\s*\"([^\"]+)\"/ ) ? $1 : ""; - return $errorstr; -} - - -sub getchecksum -{ - my $infile = shift; - - # md5 binary check - my $MD5BIN = ""; - - if ( -x "/usr/bin/md5sum" ) - { - $MD5BIN = "/usr/bin/md5sum"; - } - elsif ( -x "/sbin/md5" ) - { - $MD5BIN = "/sbin/md5 -q"; - } - - return "" if $MD5BIN eq ""; - - - my $checksum = ""; - open MD5EXE, "$MD5BIN $infile|" or return ""; - - while() - { - if (/^(\S+)\s+(\S+)$/) - { - $checksum = $1; - last; - } - elsif (/^(\S+)$/) - { - $checksum = $1; - last; - } - } - - close MD5EXE; - - return $checksum; - -} - - -sub backticks -{ - my $command = shift; - - `$command`; - return ($? == -1) ? 0 : 1; -} - - -sub bail -{ - my $str = shift; - print STDERR "$str\n" if defined $str; - - &cleanup(); - exit(1); -} - - -sub cleanup -{ - return if ($TMP eq "" || !-d $TMP); - - opendir(MAINDIR, $TMP); - my @files = readdir(MAINDIR); - closedir(MAINDIR); - - foreach my $file (@files) - { - unlink "$TMP/$file" if -e "$TMP/$file"; - } - - remove_tree($TMP); - -} - - -sub help -{ - my $str = shift; - - print <<'HELPME'; - -USAGE - ./mafftash_premafft.pl -p [FILE] - ./mafftash_premafft.pl -o [FILE] -d [DIRECTORY] - ./mafftash_premafft.pl -p [FILE] -o [FILE] -d [DIRECTORY] - - -PARAMETERS - -p [FILE] - FILE contains a list of PDBIDs (one entry per line); make sure that the PDBIDs are in the standard 5-character pdbid+chain naming format - - -o [FILE] -d [DIRECTORY] - FILE contains a list of IDs from your own structure/pdb files (one entry per line) - for each ID in the list make sure that a corresponding structure file (same ID with .pdb extension) is stored in DIRECTORY - - -h [HATFILE] - save the output hat3 file in HATFILE; if not set, the output is written to a file named 'hat3' in your current directory - - -i [INSTRFILE] - save the output instr file in INSTRFILE; if not set, the output is written to a file named 'instr' in your current directory - -HELPME - - &bail($str); -} - - - diff --git a/aphylogeo/bin/mafft-win/usr/lib/mafft/maffttext2hex.exe b/aphylogeo/bin/mafft-win/usr/lib/mafft/maffttext2hex.exe deleted file mode 100644 index 54723b64..00000000 Binary files a/aphylogeo/bin/mafft-win/usr/lib/mafft/maffttext2hex.exe and /dev/null differ diff --git a/aphylogeo/bin/mafft-win/usr/lib/mafft/makedirectionlist.exe b/aphylogeo/bin/mafft-win/usr/lib/mafft/makedirectionlist.exe deleted file mode 100644 index 265174c6..00000000 Binary files a/aphylogeo/bin/mafft-win/usr/lib/mafft/makedirectionlist.exe and /dev/null differ diff --git a/aphylogeo/bin/mafft-win/usr/lib/mafft/mccaskillwrap.exe b/aphylogeo/bin/mafft-win/usr/lib/mafft/mccaskillwrap.exe deleted file mode 100644 index f224d6b7..00000000 Binary files a/aphylogeo/bin/mafft-win/usr/lib/mafft/mccaskillwrap.exe and /dev/null differ diff --git a/aphylogeo/bin/mafft-win/usr/lib/mafft/multi2hat3s.exe b/aphylogeo/bin/mafft-win/usr/lib/mafft/multi2hat3s.exe deleted file mode 100644 index 8826242b..00000000 Binary files a/aphylogeo/bin/mafft-win/usr/lib/mafft/multi2hat3s.exe and /dev/null differ diff --git a/aphylogeo/bin/mafft-win/usr/lib/mafft/nodepair.exe b/aphylogeo/bin/mafft-win/usr/lib/mafft/nodepair.exe deleted file mode 100644 index 4757ee7a..00000000 Binary files a/aphylogeo/bin/mafft-win/usr/lib/mafft/nodepair.exe and /dev/null differ diff --git a/aphylogeo/bin/mafft-win/usr/lib/mafft/pairash.exe b/aphylogeo/bin/mafft-win/usr/lib/mafft/pairash.exe deleted file mode 100644 index 9a094ad3..00000000 Binary files a/aphylogeo/bin/mafft-win/usr/lib/mafft/pairash.exe and /dev/null differ diff --git a/aphylogeo/bin/mafft-win/usr/lib/mafft/pairlocalalign.exe b/aphylogeo/bin/mafft-win/usr/lib/mafft/pairlocalalign.exe deleted file mode 100644 index 877880bd..00000000 Binary files a/aphylogeo/bin/mafft-win/usr/lib/mafft/pairlocalalign.exe and /dev/null differ diff --git a/aphylogeo/bin/mafft-win/usr/lib/mafft/regtable2seq.exe b/aphylogeo/bin/mafft-win/usr/lib/mafft/regtable2seq.exe deleted file mode 100644 index f4bd9805..00000000 Binary files a/aphylogeo/bin/mafft-win/usr/lib/mafft/regtable2seq.exe and /dev/null differ diff --git a/aphylogeo/bin/mafft-win/usr/lib/mafft/replaceu.exe b/aphylogeo/bin/mafft-win/usr/lib/mafft/replaceu.exe deleted file mode 100644 index f4ed751a..00000000 Binary files a/aphylogeo/bin/mafft-win/usr/lib/mafft/replaceu.exe and /dev/null differ diff --git a/aphylogeo/bin/mafft-win/usr/lib/mafft/restoreu.exe b/aphylogeo/bin/mafft-win/usr/lib/mafft/restoreu.exe deleted file mode 100644 index b5c43f9a..00000000 Binary files a/aphylogeo/bin/mafft-win/usr/lib/mafft/restoreu.exe and /dev/null differ diff --git a/aphylogeo/bin/mafft-win/usr/lib/mafft/score.exe b/aphylogeo/bin/mafft-win/usr/lib/mafft/score.exe deleted file mode 100644 index 8559852b..00000000 Binary files a/aphylogeo/bin/mafft-win/usr/lib/mafft/score.exe and /dev/null differ diff --git a/aphylogeo/bin/mafft-win/usr/lib/mafft/seekquencer_premafft.pl b/aphylogeo/bin/mafft-win/usr/lib/mafft/seekquencer_premafft.pl deleted file mode 100644 index a9040fdd..00000000 --- a/aphylogeo/bin/mafft-win/usr/lib/mafft/seekquencer_premafft.pl +++ /dev/null @@ -1,600 +0,0 @@ -#!/usr/bin/perl - -#################################################################################### -# Author: KM Amada (kmamada@ifrec.osaka-u.ac.jp) -# -# Ver. Date Changelog -#################################################################################### -# 1.0 11.01.13 Initial release -# -# **Skipped version 2 to standardise version numbers to seekquencer.pl script** -# -# 3.0 04.24.14 Added split option -mod for output -# Uses seekquencer_v3 backend -# -# 4.0 05.12.14 Added new options: -run -trd -noin -# Sets -seqa fast in seekquencer.pl -# Uses seekquencer_v4 backend -# -# 4.1 05.19.14 Added a check on running REST requests before proceeding -# to avoid server load problems -# -# 4.2 05.27.14 Seq limit processing done in seekquencer.pl script -# to avoid server load problems -# -# 4.3 07.22.14 Added new option: -seqd -# Blast limit changed from factor of 10 to -blim option -# Timing on sleep changed; added srand() for making seed -# Moved the job limit processing to server side -# -# 4.4 08.05.14 Modified to work in multiple OS -# -# -#################################################################################### - -use strict; -use Getopt::Long; -use File::Path qw(make_path remove_tree); -use Cwd; -use LWP::Simple; -use LWP::UserAgent; - -# to prevent error: Header line too long (limit is 8192) -use LWP::Protocol::http; -push(@LWP::Protocol::http::EXTRA_SOCK_OPTS, MaxLineLength => 0); - - - -my $BASEURL = "http://sysimm.ifrec.osaka-u.ac.jp/seekquencer/REST/service.cgi/premafft"; -my ( $INPUTFILE, $IDLISTFILE, $SEQFASTAFILE, $OUTPUTFILE, $SEQFLAG, $STRFLAG, $EVALFLAG, $NOINFLAG ); -my $OUTTYPE = "mafftash"; - -my $SEQDATABASE = "uniref100"; -my $SEQLIMIT = 100; -my $SEQBLASTLIMIT = 100; - -my $RUNMODE = "normal"; # thread|normal -my $THREADCOUNT = 3; - - -GetOptions -( - 'inp=s' => \$INPUTFILE, - 'idf=s' => \$IDLISTFILE, - 'seqf=s' => \$SEQFASTAFILE, - 'out=s' => \$OUTPUTFILE, - 'str' => \$STRFLAG, - 'seq' => \$SEQFLAG, - 'seqd=s' => \$SEQDATABASE, - 'lim=i' => \$SEQLIMIT, - 'blim=i' => \$SEQBLASTLIMIT, - 'pre' => \$EVALFLAG, - 'noin' => \$NOINFLAG, - 'mod=s' => \$OUTTYPE, - 'run=s' => \$RUNMODE, - 'trd=i' => \$THREADCOUNT, - - -); - -my $ISWINDOWS = ( $^O =~ /^MSWin/ ) ? 1 : 0; -print STDERR "[Seekquencer-premafft 4.4 on $^O]\n"; - - -# set temp directory -my $CWD = getcwd; -my $TMP = "$CWD/seekpremafft$$"; -make_path($TMP) unless -d $TMP; - - - -###### -# validation -help("Required parameter: define input as '-inp' or '-idf' or '-seqf'") if ( !defined $INPUTFILE && !defined $IDLISTFILE && !defined $SEQFASTAFILE ); -help("'-inp' is already defined") if ( defined $INPUTFILE && (defined $IDLISTFILE || defined $SEQFASTAFILE) ); -help("Input file $INPUTFILE does not exist (or filesize is 0)") if ( defined $INPUTFILE && (! -e $INPUTFILE || !-s $INPUTFILE) ); -help("Input file $IDLISTFILE does not exist (or filesize is 0)") if ( defined $IDLISTFILE && (! -e $IDLISTFILE || !-s $IDLISTFILE) ); -help("Input file $SEQFASTAFILE does not exist (or filesize is 0)") if ( defined $SEQFASTAFILE && (! -e $SEQFASTAFILE || !-s $SEQFASTAFILE) ); -help("Required parameter: output file '-out'") unless ( defined $OUTPUTFILE ); -help("Set either '-str' or '-seq' or dont set any at all") if ( defined $STRFLAG && defined $SEQFLAG ); - -help("Invalid value for '-seqd '") if ( $SEQDATABASE ne "uniref100" && $SEQDATABASE ne "uniref90" && $SEQDATABASE ne "uniref70" && $SEQDATABASE ne "uniprot"); -help("Invalid value for '-mod '") if ( $OUTTYPE ne "fasta" && $OUTTYPE ne "mafftash" && $OUTTYPE ne "mafftash-split" ); -help("Invalid value for '-run '") if ( $RUNMODE ne "thread" && $RUNMODE ne "normal" ); -help("Invalid value for '-trd '; count should be between 1 and 5 (inclusive)") if ( $RUNMODE eq "thread" && ($THREADCOUNT <= 0 || $THREADCOUNT > 5) ); - - -###### -# check existing requests -print STDERR "Checking server status...\n"; - -# generate seed -srand($$); - -# sleep a bit to give time for lsf response -sleep(int(rand(6))+1); - - -my $browser = LWP::UserAgent->new; -$browser->timeout(0); - -# get: check if you can send a new request this time -my $jobsResponse = $browser->get("$BASEURL/isAllowed"); - -if ( $jobsResponse->is_success ) -{ - my $status = parseJobQueryResponse($jobsResponse->content); - bail("Max jobs reached. The server cannot process your request right now; try again later.", 0) unless $status > 0; -} -else -{ - bail(sprintf("[%d] %s\n", $jobsResponse->code, parseError($jobsResponse->content))); -} - - -###### -# make a temporary input if lists were provided -unless ( defined $INPUTFILE ) -{ - $INPUTFILE = "$TMP/input.homemade"; - open INPF, ">$INPUTFILE" or bail("Error writing to input file."); - - if ( defined $IDLISTFILE ) - { - open IDLIST, "<$IDLISTFILE" or bail("Error reading input file."); - while( ) - { - chomp; - if ( /(\w{5})/ ) - { - print INPF ">PDBID\n$1\n"; - } - } - close IDLIST; - } - - - if ( defined $SEQFASTAFILE ) - { - open FASTA, "<$SEQFASTAFILE" or bail("Error reading input file."); - while( ) - { - chomp; - print INPF "$_\n"; - } - close FASTA; - } - - close INPF; -} - - -###### -# prepare parameters -print STDERR "Preparing parameters for service request...\n"; - -my @parameters = (); -push(@parameters, "fileinput" => ["$INPUTFILE"]); -push(@parameters, "out_type" => $OUTTYPE); - -push(@parameters, "rest_flag" => "1"); -push(@parameters, "cls_flag" => "1"); -push(@parameters, "pre_flag" => "1") if defined $EVALFLAG; -push(@parameters, "noin_flag" => "1") if defined $NOINFLAG; - -push(@parameters, "run_mode" => $RUNMODE); -push(@parameters, "thread_count" => $THREADCOUNT) if $RUNMODE eq "thread"; - - -if ( defined $STRFLAG ) -{ - push(@parameters, "str_flag" => "1"); - push(@parameters, "ash_flag" => "1"); -} -elsif ( defined $SEQFLAG ) -{ - push(@parameters, "seq_flag" => "1"); - push(@parameters, "seq_algorithm" => "fast"); - push(@parameters, "seq_database" => $SEQDATABASE); - push(@parameters, "seq_blastlimit" => $SEQBLASTLIMIT); - push(@parameters, "seq_outputlimit" => $SEQLIMIT); -} -else -{ - push(@parameters, "str_flag" => "1"); - push(@parameters, "ash_flag" => "1"); - push(@parameters, "seq_flag" => "1"); - push(@parameters, "seq_algorithm" => "fast"); - push(@parameters, "seq_database" => $SEQDATABASE); - push(@parameters, "seq_blastlimit" => $SEQBLASTLIMIT); - push(@parameters, "seq_outputlimit" => $SEQLIMIT); -} - - - -###### -# start rest service -print STDERR "Sending service request...\n"; - -# post: running a mafftash job -my $postResponse = $browser->post( $BASEURL, \@parameters, 'Content_Type' => 'form-data' ); -bail(sprintf("[%d] %s\n", $postResponse->code, parseError($postResponse->content))) unless($postResponse->is_success); - - -# get response from post request -my ($status, $seekid) = parseResponse($postResponse->content); - -my $MAXTRIES = 3; -my $STIMER = 5; -my $timer = 0; - -print STDERR "Request sent! Waiting for response...[$seekid]\n"; - -my $checklist = {}; - -# wait for results until it becomes available -while(1) -{ - # sleeps for 5+random, 10+random, 15+random, 20+random, 25+random, 30+random ,,, 60+random, 60+random,,, - $timer = $timer >= 60 ? 60 : $timer+$STIMER; - sleep($timer+int(rand(4))); - - # get: get results for mafftash job - my $getResponse = $browser->get("$BASEURL/$seekid"); - - if ( $getResponse->is_success ) - { - - # get response from get request - ($status, $seekid) = parseResponse($getResponse->content); - next unless ( $status eq "done" ); - - - # if job is finished and ready - print STDERR "Results found!\n"; - my $csfile = "$TMP/checksum"; - my $try1 = 1; - - - while(1) - { - print STDERR "Fetching Results... [Trial $try1]\n"; - - if ( is_success(getstore("$BASEURL/get/$seekid/checksum", $csfile)) && -e $csfile && -s $csfile ) - { - # get response from get request - $checklist = extractchecksum($csfile); - bail("Error retrieving list of compressed files!") unless ( scalar %$checklist > 0 ); - - - foreach my $id ( sort keys %$checklist ) - { - sleep 1; - my $checkfile = "$TMP/$id"; - my $checkid = $checklist->{$id}; - my $try2 = 1; - - while(1) - { - unlink $checkfile if -e $checkfile; - - if ( is_success(getstore("$BASEURL/get/$seekid/$id", $checkfile)) && -e $checkfile && -s $checkfile ) - { - last if $ISWINDOWS; - - my $hashid = getchecksum($checkfile); - #print STDERR "[hashid]$hashid [checkid]$checkid\n"; - - if ($hashid ne "" && $hashid ne $checkid ) - { - #unlink $checkfile if -e $checkfile; - bail("Error retrieving compressed file from server! [Checksum Failed]") if $try2 >= $MAXTRIES; - $try2++; - sleep $STIMER; - } - else - { - last; - } - } - else - { - bail("Error retrieving compressed file from server!") if $try2 >= $MAXTRIES; - $try2++; - sleep $STIMER; - } - } - } - - last; - } - else - { - bail("Error retrieving list of compressed files from server!") if $try1 >= $MAXTRIES; - $try1++; - sleep $STIMER; - } - } - - last; - - } - else - { - bail(sprintf("[%d] %s\n", $getResponse->code, parseError($getResponse->content))); - } - -} - - -# make sure outputs were generated -# decompress -print STDERR "Assembling final results...\n"; - -foreach my $id ( sort keys %$checklist ) -{ - if ( $id =~ /^$seekid\.out(\.str|\.seq)?/ ) - { - bail("Error: Output file corrupted!") unless -e "$TMP/$id"; - appendToFile("$TMP/$id","$OUTPUTFILE".$1); - } -} - -cleanup(); - - - -#################### -#################### - - -sub parseResponse -{ - my $response = shift; - my $status = ""; - my $seekid = ""; - - if ( $response =~ /^([^\s:]+):([^\s:]+)$/ ) - { - $seekid = $1; - $status = $2; - } - - return ($status, $seekid); -} - - -sub parseJobQueryResponse -{ - my $response = shift; - my $jobs = 100; - - if ( $response =~ /^(\d+)$/ ) - { - $jobs = $1; - } - - return $jobs; -} - - -sub extractchecksum -{ - my $infile = shift; - my %dataset = (); - - #open CSUM, "tar -zxf $infile -O|" or return \%dataset; - open CSUM, "<$infile" or return \%dataset; - - while() - { - chomp; - if ( /^(\S+)\s+(\S+)$/ ) - { - $dataset{$2} = $1; - } - } - - close CSUM; - - return \%dataset; -} - - -sub parseError -{ - my $response = shift; - - #"error":"Invalid number of inputs found." - my $errorstr = ( $response =~ /\"error\"\s*:\s*\"([^\"]+)\"/ ) ? $1 : $response; - return $errorstr; -} - - -sub getchecksum -{ - my $infile = shift; - - # md5 binary check - my $MD5BIN = ""; - - if ( -x "/usr/bin/md5sum" ) - { - $MD5BIN = "/usr/bin/md5sum"; - } - elsif ( -x "/sbin/md5" ) - { - $MD5BIN = "/sbin/md5 -q"; - } - - return "" if $MD5BIN eq ""; - - - my $checksum = ""; - open MD5EXE, "$MD5BIN $infile|" or return ""; - - while() - { - if (/^(\S+)\s+(\S+)$/) - { - $checksum = $1; - last; - } - elsif (/^(\S+)$/) - { - $checksum = $1; - last; - } - } - - close MD5EXE; - - return $checksum; - -} - - -sub backticks -{ - my $command = shift; - - `$command`; - return ($? == -1) ? 0 : 1; -} - - -sub bail -{ - my $str = shift; - my $status = shift; - - #0 for success and 1 for error - $status = 1 unless defined; - - print STDERR "$str\n" if defined $str; - - cleanup(); - - exit($status); -} - - -sub cleanup -{ - return if ($TMP eq "" || !-d $TMP); - - opendir(MAINDIR, $TMP); - my @files = readdir(MAINDIR); - closedir(MAINDIR); - - foreach my $file (@files) - { - unlink "$TMP/$file" if -e "$TMP/$file"; - } - - remove_tree($TMP); - -} - - -sub appendToFile -{ - my $inpfile = shift; - my $outfile = shift; - - open INPF, "<$inpfile" or bail("Server Error: Error in reading file."); - open OUTF, ">>$outfile" or bail("Server Error: Error in writing to file."); - - while() - { - print OUTF $_; - } - - close OUTF; - close INPF; -} - - - -sub help -{ - my $str = shift; - - print <<'HELPME'; - -USAGE - ./seekquencer_premafft.pl -inp -out [-str|-seq] - ./seekquencer_premafft.pl -idf -seqf -out [-str|-seq] - - -PARAMETERS - -inp - INFILE is a FASTA-formatted file - PDB entries are written as: - >PDBID - [5-character pdbid+chain] - - While sequence entries are written as: - >[id] - [sequence] - - -idf - IDLISTFILE is a file containing a list of pdbids - pdbids should be a 5-character pdbid + chain - - -seqf - SEQFASTA is a fasta file - entries are written as: - >[id] - [sequence] - - -out - Results are writen to a file named OUTFILE - - -str - Only structures will be collected by Seekquencer - If neither -str nor -seq is set, both structures and sequences will be collected by Seekquencer - - -seq - Only sequences will be collected by Seekquencer - If neither -str nor -seq is set, both structures and sequences will be collected by Seekquencer - - -OPTIONAL PARAMETERS: - -seqd - Search Database for sequence homologs. Default value: uniref100 - - -lim - this sets the maximum number of sequence homologs collected. Default value: 100 - - -blim - this sets the -b and -v value when running blastall. Default value: 100 - - -pre - When -str is set, this will compare all structures against all using pdp-ash - This would ensure that all structures collected are matching - All structures that do not match will be removed - - -noin - When set, inputs will not be included in the output - - -mod - Defines the output format - mafftash (default) will print a mafftash-formatted fasta file - mafftash-split will make 2 files separating the structures (OUTFILE.str) from sequences (OUTFILE.seq) - fasta will print a regular fasta file - - -run - thread will run simultaneous jobs during blast queries (faster but takes more nodes) - normal will run sequential blast queries (slower but takes less nodes) - Default value: normal - - -trd - if -run is defined, this sets the number of parallel jobs to run. Default value: 3 - - -HELPME - - bail($str); -} - diff --git a/aphylogeo/bin/mafft-win/usr/lib/mafft/seq2regtable.exe b/aphylogeo/bin/mafft-win/usr/lib/mafft/seq2regtable.exe deleted file mode 100644 index 1d9b4763..00000000 Binary files a/aphylogeo/bin/mafft-win/usr/lib/mafft/seq2regtable.exe and /dev/null differ diff --git a/aphylogeo/bin/mafft-win/usr/lib/mafft/setcore.exe b/aphylogeo/bin/mafft-win/usr/lib/mafft/setcore.exe deleted file mode 100644 index a1225385..00000000 Binary files a/aphylogeo/bin/mafft-win/usr/lib/mafft/setcore.exe and /dev/null differ diff --git a/aphylogeo/bin/mafft-win/usr/lib/mafft/setdirection.exe b/aphylogeo/bin/mafft-win/usr/lib/mafft/setdirection.exe deleted file mode 100644 index 15ebfefe..00000000 Binary files a/aphylogeo/bin/mafft-win/usr/lib/mafft/setdirection.exe and /dev/null differ diff --git a/aphylogeo/bin/mafft-win/usr/lib/mafft/sextet5.exe b/aphylogeo/bin/mafft-win/usr/lib/mafft/sextet5.exe deleted file mode 100644 index a0cd8e89..00000000 Binary files a/aphylogeo/bin/mafft-win/usr/lib/mafft/sextet5.exe and /dev/null differ diff --git a/aphylogeo/bin/mafft-win/usr/lib/mafft/splittbfast.exe b/aphylogeo/bin/mafft-win/usr/lib/mafft/splittbfast.exe deleted file mode 100644 index cfe41910..00000000 Binary files a/aphylogeo/bin/mafft-win/usr/lib/mafft/splittbfast.exe and /dev/null differ diff --git a/aphylogeo/bin/mafft-win/usr/lib/mafft/tbfast.exe b/aphylogeo/bin/mafft-win/usr/lib/mafft/tbfast.exe deleted file mode 100644 index c8434ff8..00000000 Binary files a/aphylogeo/bin/mafft-win/usr/lib/mafft/tbfast.exe and /dev/null differ diff --git a/aphylogeo/bin/mafft-win/usr/lib/mafft/version.exe b/aphylogeo/bin/mafft-win/usr/lib/mafft/version.exe deleted file mode 100644 index 29afed62..00000000 Binary files a/aphylogeo/bin/mafft-win/usr/lib/mafft/version.exe and /dev/null differ diff --git a/aphylogeo/bin/mafft-win/usr/share/misc/magic b/aphylogeo/bin/mafft-win/usr/share/misc/magic deleted file mode 100644 index e69de29b..00000000 diff --git a/aphylogeo/bin/muscle5.1.linux_intel64 b/aphylogeo/bin/muscle5.1.linux_intel64 deleted file mode 100755 index 63fe0ef5..00000000 Binary files a/aphylogeo/bin/muscle5.1.linux_intel64 and /dev/null differ diff --git a/aphylogeo/bin/muscle5.1.win64.exe b/aphylogeo/bin/muscle5.1.win64.exe deleted file mode 100644 index c9cacda5..00000000 Binary files a/aphylogeo/bin/muscle5.1.win64.exe and /dev/null differ diff --git a/aphylogeo/bin/tmp/a.out b/aphylogeo/bin/tmp/a.out deleted file mode 100644 index e69de29b..00000000