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:[0,34],hyrax:5,icod:[33,34,60],idea:[0,3,11,34,40,41,44,66,94],ident:[6,8,10,11,20,34],identif:5,identifi:[0,5],idlist:5,idx:[3,25,70],if_:37,iff:37,ignor:[1,3,5,11,35,38,44,61,75,90],ignore_internal_nod:61,iii:[8,49,62],ijkl:37,illumina:[1,17],illumina_sequ:1,illustr:[5,6,9,13,14,26,27,38,43,44,53,58,61,62,74,75,78,80,81,90,94],imag:38,immedi:[62,74],immut:[1,24,35,61],impact:61,implement:[0,1,3,5,13,15,25,37],impli:[0,8,36,74,93,94],implicit:60,implicitli:60,importantli:[61,94],impos:[0,1],imposs:75,improv:[1,2,11,20,30],impun:3,in1:94,in2:94,in_fil:3,in_file_nam:3,inabl:0,inaccur:[0,56],inadequ:44,inadvert:1,inc:[0,36],incid:6,incident:[0,93],incl:44,includ:[0,1,3,5,6,8,9,10,21,26,31,32,36,38,40,44,45,51,55,61,64,74,80,93],include_head:43,incomplet:[6,21,74],incomplete_terminal_codon_vari:74,inconsist:3,inconveni:3,incorpor:[0,8,44],incorrect:[1,3,5],incorrectli:1,increas:[1,3,80],incred:5,indel_posit:1,indent:[3,36,94],independ:[0,8,31,38,58],index:[1,3,4,10,20,31],indic:[0,1,2,3,4,6,7,31],indirect:93,indirectli:[0,44],individu:[0,3],induc:[0,5],inexact:74,infer:[6,22],infern:1,infil:[3,5,44,57],infile_nam:3,infilenam:3,influenc:[31,67,74],info:[5,22,75],inform:[0,1,3,5,11,15,22,24],infrequ:94,infring:0,ing:1,inherit:[1,44,45,60,65,74],init:[3,38,49,62,80],initi:[1,3,8,34,37,38],inlcud:44,inner:[1,3,35,61],inner_join:61,input1:57,input2:57,input:[1,3,8,13,31,32,41,42],input_dir:94,input_f:94,input_fp:94,input_handl:44,input_param:57,inputhandl:44,inputparam:57,insect:61,insensit:[5,20],inseq:[10,39],inseqs_protein:[10,39],insert:1,insid:3,instal:[0,1],instanc:[1,3,5,6,7,9,25,31,32],instanti:[1,44,74],instead:[0,1,3,5,6,9,10,11,25,34,36,38,44,45,57,61,65,72,82],instruct:[2,10,40],intact:0,integr:[0,3,37,44,91],intend:[0,24,36,44],intens:27,intent:0,interact:[0,3,11,36,44,45,94],interchang:0,interest:[0,4,6,11,31,34,37,38,44,60,62,71,74,80,94],interfac:[0,1,2,3,5,22,37,44,72,74,77],intergenic_vari:74,interleav:[37,54,64],intermolecular:50,intern:[3,5,14,28,30,44,60,65,74],internet:[36,92],interpret:[3,32,36,45,50],interrupt:[14,93],interv:1,intervent:[5,44],intestinali:65,intramolecular:[20,23],introduc:[0,1,12,41,53,60,61],intron:1,intuit:94,invalid:[0,50,61,94],invent:3,inversedict:[3,37],inversedictmulti:37,invert:20,investig:[44,45],invok:[27,36,44,61],involv:[28,30,32],ioerror:94,ipdft:71,ipdft_pow:71,ipldfdk:10,is_:34,is_char:37,is_clad:[38,49,80],is_const:[38,49,62,76,80],is_independ:[38,52,67,77,78,80,87,90],is_iter:37,is_not:34,is_numer:61,is_protein:10,is_stem:80,isgap:6,isi:61,isinst:[9,37,44,61],isn:[37,40],isoff:44,isoleucin:58,isomd:1,ison:[44,45],ispair:3,ispath:[44,45],issu:[0,1,11,21,24,61,74,91],istip:[28,30],isvalid:[24,43],iswritten:[44,45],item:[0,1,3],itemwis:51,iter:[1,3,5],iternontip:[28,30],iterposit:6,itertip:[28,30,65],itni:12,itself:[0,1,3],iupac:66,iupac_dna_ambigu:24,iupac_dna_ambiguities_compl:24,iupac_dna_char:24,iupac_protein_ambigu:24,iupac_protein_char:24,iupac_rna_ambigu:24,iupac_rna_ambiguities_compl:24,iupac_rna_char:24,iupacconsensu:66,jaccard:1,jackknif:[1,20],jackknifestat:31,jackrabbit:72,jame:0,jan:1,januari:5,jc69:38,jeremi:66,jess:8,jim:3,job:[5,57],john:36,join:1,jone:38,journal:[5,61],jpg:44,jtt92:[38,64,72],judg:58,judgment:0,juke:1,jul:94,julia:[82,83,84],julien:71,june:0,just:[3,5,6,9,10,14],just_constant_aln:6,just_nuc:6,just_seqs_pars:44,just_variable_aln:6,justif:61,justifi:61,justin:[70,89],k80:38,kappa:[12,38],kappa_bin_submod:62,kappa_hi:38,kappa_lo:38,kappa_ml:38,keep:[0,3,10,34,49,51,72,74,94],kei:[3,4,5,6,8,10,18,20,32,33,34],kendal:[1,31],kendall_correl:31,kept:[13,72],kernel:0,key_list:10,keyerror:[6,33,60],keyword:[1,3,5,6,22,31,36],kimura:[57,73],kind:[0,2,5,24,93],klara:1,klebsormidiophycea:11,knight:[58,75,91],know:[0,5,6,10,24,25,31,36,40,44,49,51,55,60,61,62,74,76,81,87],known:[3,5,25,31,44,62],kosinski:1,kqiqesgesgslaarqerqaqvnlt:[12,41],kqiqessengslaarqerqaqvnlt:[12,41],krcv:58,krcvwdek:58,kristian:33,kruskal:59,kuczynski:[70,89],kwarg:1,lab:[74,91],label:[1,3,15,17],label_pars:22,label_templ:52,label_to_nam:[11,22],labelpars:22,lack:[3,65],lambda:[5,6,11,17,22,35,37,61,62],landmark:25,languag:[0,2,36],larg:[1,3,11],largecon:35,larger:[5,59,61,72],largest:20,last:[1,3,6,9,14,18,20,25],lastcommonancestor:[28,30],lastz_net:74,later:[0,3,11,36,37,38,44,49,51,52,60,61,67,74,77,78],latest:1,latin:[22,74],latin_nam:5,latin_to_common:[5,22],latinnam:5,latter:[1,3,27,38,40,49,71,74,78,94],lattic:[1,32],law:0,layout:11,lcl:10,lead:[3,15,80],leaf:1,learn:3,least:[0,3],least_squar:[13,14,72],leav:[3,5,36,44,45,61,72,74,94],left:[3,9,20],legaci:[10,45],legal:0,legend:[1,61],len:[4,5,6,11,18,25,27,31,33,37,38,43,51,55,61,66,71,72,74,75,87],lend:3,length:[1,5,6,8,9,10,12,15,25,28],less:[5,6,59,66],let:[8,10,25,32,36,40,42,43,44,55,57,58,59,60,61,65,66,72,73,82,83],letter:[3,54,60],level:[1,3,5,20,24,31,32,33],lf_bin:62,lf_kappa:62,lf_one:62,lf_patch:62,liabil:93,liabl:[0,93],librari:[0,1,2,34,91,94],license:0,licensor:0,lie:37,lieu:22,lift:45,ligand: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License","Changelog","The Readme","Coding guidelines","DNA and RNA sequences","Accessing databases","Collections and Alignments","Alphabets","Analysis of sequence composition","Annotations","Controlling BLAST","Building a tree of life","Building alignments","Building phylogenies","Checkpointing optimisation runs","Community analysis","Controlling third party applications","Dealing with HTS data","Getting a genetic code","HPC environments","PyCogent Cookbook","Introduction","Loading nucleotide, protein sequences","Manipulating biological data","Using the <code class=\"docutils literal\"><span class=\"pre\">MolType</span></code> and <code class=\"docutils literal\"><span class=\"pre\">Sequence</span></code> objects","Multivariate data analysis","Distribution of tasks across multiple CPUs using <code class=\"docutils literal\"><span class=\"pre\">mpi</span></code>","Distribution of tasks across multiple CPUs using <code class=\"docutils literal\"><span class=\"pre\">multiprocess</span></code>","Phylonodes Methods","Protein sequences","Trees","Standard statistical analyses","Intramolecular contacts","Structural data","Structural Data Advanced","Tabular data","Tips for using python","Useful Utilities","Evolutionary analysis using likelihood","The data files used in the documentation","For Developers","Map protein alignment gaps to DNA alignment gaps","Using alignment application controllers to align unaligned sequences","Creating and manipulating alignment profiles","Application Controller Documentation","Building and using a new application controller","Make a UPGMA cluster","Make a neighbor joining tree","Calculate pairwise distances between sequences","Using codon models","Perform a coevolutionary analysis on biological sequence alignments","Complete version of manipulating sequence annotations","Drawing dendrograms and saving to PDF","Drawing a dotplot","Use an empirical protein substitution model","Selecting and grouping entities","Estimate parameter values using a sampling from a dataset","Generating application commandlines","Compute the effect of a nucleotide substitution on residue polarity in two different genetic codes using GeneticCode and AAIndex","The <code class=\"docutils literal\"><span class=\"pre\">goodness_of_fit</span></code> module","Working with macromolecular structures","Data Manipulation using <code class=\"docutils literal\"><span class=\"pre\">Table</span></code>","Evaluate process heterogeneity using a Hidden Markov Model","Cogent Usage Examples","Making a phylogenetic tree from a protein sequence alignment","Manipulation of Tree Node Objects","Motif results example","A test of the neutral theory","Performing a parametric bootstrap","Perform Principal Coordinates Analysis","Perform Nonmetric Multidimensional Scaling","Estimating periodic signals","Phylogenetic reconstruction by least squares","Using phylogeny application controllers to construct phylogenetic trees from alignments","Querying Ensembl","Querying NCBI for VWF","Analysis of rate heterogeneity","Performing a relative rate test","Reusing results to speed up optimisation","Getting the reverse complement","Allowing substitution model parameters to differ between branches","Advanced sequence handling","Seqsim Simple Alignment Simulation Example","Seqsim Alignment Simulation Example with Non-standard alphabet","Seqsim Simple Tree Simulation","The simplest script","Simulate an alignment","Likelihood analysis of multiple loci","Translating DNA into protein","Run a Fast Unifrac community analysis","Specifying and using an unrestricted nucleotide substitution model","Welcome to PyCogent&#8217;s documentation!","Quick installation using pip","Licenses and disclaimer","Scripting guidelines"],titleterms:{"1st":4,"2nd":4,"3rd":[4,6,12,13,63],"abstract":5,"case":37,"char":37,"class":[37,44,45,62],"export":[35,61],"function":[6,36,37,38,55],"new":[1,6,33,35,40,44,45,91,94],"return":[4,34,37],"short":34,aaindex:58,abbrevi:3,about:[33,44],absent:9,accept:3,access:[5,6,33],account:74,acid:[9,18,34],across:[26,27],add:33,addannot:9,addfeatur:9,advanc:[34,81],aikak:38,alanin:34,align:[5,6,9,11,12,16,22,38,41,42,43,50,64,73,74,82,83,86],all:[5,6,9,18,28,30,33,34,37,92],allow:[24,80],alpha:15,alphabet:[7,33,83],altern:[22,80],altloc:33,amino:[18,34],analys:[8,31,33,74],analysi:[8,15,25,38,50,52,63,69,76,87,89],ancestor:[28,30],ancestr:38,angl:33,annot:[9,51],announc:91,apart:[28,30],app:[12,13,16,44],append:[6,35,61],appli:15,applic:[16,37,42,44,45,57,63,73,80],appresult:44,arbitrari:6,argument:80,ascii:30,asciiart:[28,30],asonespan:9,assess:72,associ:31,asymmetr:32,atom:33,auto:[62,71],autom:9,avail:[5,9,74],bacteri:5,balanc:30,base:[6,8,15,31,44,55],basic:[6,28,30,44],bayesian:38,bedgraph:[35,61],behaviour:9,best:72,beta:15,between:[15,28,30,33,37,48,80],bifurc:30,binomi:31,biolog:[23,50],blast:[10,16],bootstrap:[38,68],bound:38,branch:[30,49,52,80],brief:44,bug:1,build:[11,12,13,38,40,45],built:13,calckruskalstress:59,calcsstress:59,calcul:[6,15,30,33,48],call:3,can:[9,18,38],canon:[5,33],capabl:[35,92],caution:8,center:33,certain:9,chain:[33,34],chang:[1,4,35],changelog:1,charact:[6,22],check:[36,37,38],checklist:40,checkpoint:[14,38],chi:31,children:[28,30,34],choic:[38,94],citat:91,clade:80,clean:44,clustalw:[12,16],cluster:[25,46],code:[3,18,23,33,58,92],codebas:94,codon:[4,6,8,12,18,38,49],codonalphabet:18,coevolutionari:50,cogent:[1,12,44,63],collect:[6,22],column:[6,35,61],combin:37,command:[44,94],commandlin:[44,57],comment:3,common:[28,30],commun:[15,89],compar:[8,30,74],comparison:34,complement:[4,79],complementar:4,complet:[44,51],compon:61,composit:8,comput:[6,15,58,63],condit:65,confid:38,connect:[5,28,30],consid:33,constant:[6,38],constrain:37,construct:[6,9,33,37,49,73],constructor:22,contact:[32,91],contain:[33,37],content:8,contigu:6,continu:71,contribut:91,control:[10,16,42,44,45,63,73],convent:3,convers:61,convert:[4,6,7,12,17,18,29,37],cookbook:20,coordin:[5,9,25,33,69,74],copi:[9,30,34],core:94,correct:18,correl:[31,62,71],correspond:18,count:[33,35,61],cover:55,cpg:5,cpu:[26,27],creat:[4,6,7,9,29,30,33,35,37,43,44,94],creation:61,credit:11,criterion:38,curri:37,custom:[9,61,94],customis:9,data:[17,23,25,31,33,34,35,37,39,44,61,63,71],databas:5,dataset:56,deal:17,decid:45,deepli:37,defin:[44,45,61,94],deleg:37,delimit:[35,37],dendrogram:52,depend:[2,92],descript:5,design:[44,94],detail:5,determin:[37,38],develop:[40,44,92],deviat:31,dict:22,dictionari:[33,37,94],differ:[15,31,37,58,80],digit:35,dihedr:33,dinucleotid:8,dir:36,directli:[9,33],directori:44,disclaim:93,discontinu:9,discret:71,displai:[9,35],distanc:[8,13,15,28,30,33,37,48],distinct:35,distribut:[26,27,31,62],divers:15,dna:[4,18,24,29,41,88],dnasequ:[4,18],document:[1,36,39,40,44,63,91,94],doe:33,dotplot:53,download:11,draw:[52,53],each:[30,33,37,61],edg:[28,30,80],efetch:5,effect:58,element:[5,6],elimin:6,els:37,empir:54,ensembl:[5,74,92],entir:61,entiti:[33,34,55,60],entri:[5,33],environ:[11,19],est:74,estim:[13,38,56,71],etc:33,euclidean:33,eutil:5,evalu:62,everyth:9,evolut:63,evolutionari:38,evolv:62,exampl:[3,34,44,63,65,66,82,83,94],exist:[6,16,33,34,35],exon:5,extend:61,extens:40,extra:11,extract:[6,37],farthest:[28,30],fast:[13,25,62,89],fasta:[4,5,6,22],fastq:17,fasttre:[11,13],featur:[1,5,9,34],fetch:5,file:[3,5,6,9,17,22,28,29,30,33,35,37,39],filepath:44,filter:[6,11,35,61],find:[5,18,32,37],first:[5,18,37,94],fit:[37,38,72],fix:1,flag:94,flagparamet:44,flat:33,flatten:37,forc:37,format:[3,4,6,17,22,28,30,35,61],formatdb:45,fourier:71,fraction:6,frame:18,framework:44,free:38,friend:44,from:[4,5,6,9,11,12,13,18,22,28,29,30,33,34,35,37,40,56,64,73],full:30,further:36,gamma:62,gap:[4,6,9,11,12,24,41],genbank:[5,9],gene:[5,74],gener:[13,57,63,94],genet:[18,23,58],geneticcod:58,genom:[5,74],genpept:5,geometr:33,get:[4,5,6,9,18,28,30,31,33,35,36,37,38,74,79],github:40,give:37,given:[28,30],goodness_of_fit:59,grab:[18,40],group:[18,37,55],guidelin:[3,94],gzip:37,halt_exec:44,handl:[6,22,44,81],have:[9,33,34,37],head:35,header:33,heat:31,hello:36,help:36,heteroatom:33,heterogen:[38,49,62,76],hidden:62,hide:37,hierarch:25,hierarchi:[55,60],highli:11,histogram:31,hmm:38,host:74,how:[3,18,33,38,94],hpc:19,hypothes:38,ident:[37,60],identifi:6,implement:44,improv:38,includ:94,independ:62,index:37,indic:35,individu:[6,28,30],inform:[33,38],initi:44,input:44,insensit:37,insert:[6,33],insid:34,inspect:5,instal:[2,92],instanc:[34,44],integ:[7,30],interfac:94,interrog:74,interv:[5,38],intramolecular:32,introduct:[9,21],intron:5,invers:31,invert:37,involv:35,island:5,item:[9,37],iter:[6,33,35,37,61],itself:9,jackknif:31,join:[4,35,47,61],just:[18,38],kappa:62,kei:37,known:94,label:22,larg:35,largest:37,last:[28,30,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