##Obsolete software
The following programs were present in earlier version of MUMmer, but have been superseeded by other programs. They are not very useful anymore, deemed obsolete, and not maintained anymore. They are not built and would have to be built by hand.
###run-mummer1
Description:
This script is taken directly from MUMmer1.0 and is best used to align two sequences in which there is high similarity and no re- arrangements. Common use cases are: aligning two finished bacterial chromosomes. Please refer to "docs/run-mummer1.README" for the original documentation for this script and its output.
USAGE:
run-mummer1 <seq1> <seq2> <tag> [-r]
<seq1> specifies the file with the first sequence in FastA format.
No more than one sequence is allowed.
<seq2> specifies the file with the second sequence in FastA format.
No more than one sequence is allowed.
<tag> specifies the prefix to be used for the output files.
[-r] is an optional parameter that will reverse complement the
second sequence.
OUTPUT:
out.align the out.gaps file interspersed with the alignments
of the gaps.
out.errorsgaps the out.gaps file with an extra column stating the
number of errors contained in each gap.
out.gaps an ordered (clustered) list of matches with position
information, and gap distances between each match.
out.out a list of all maximal unique matches between the two
input sequences ordered by their start position in the
second sequence.
Notes:
All output coordinates reference their respective strand. This means that if the -r switch is active, coordinates that reference the second sequence will be relative to the reverse complement of the second sequence. Please use nucmer or promer if this coordinate system is confusing.
Eventually, this script's components will be rewritten to work with the new MUMmer format standards and phased out in favor of the new components and wrapping script.
###run-mummer3
Description:
This script is the improved version of the MUMmer1.0 run-mummer1 script. It uses a new clustering algorithm that appropriately handles multiple sequence rearrangements and inversions. Because of this, it can handle more divergent sequences better than run-mummer1. In addition, it allows a multi-FastA query file for 1-vs-many sequence comparisons. Please refer to "docs/run-mummer3.README" for more detailed documentation of this script and its output.
USAGE:
run-mummer3 <reference> <query> <prefix>
<reference> specifies the file with the reference sequence in FastA
format. No more than one sequence is allowed.
<query> specifies the multi-FastA sequence file that contains
the query sequences.
<prefix> specifies the file prefix for the output files.
OUTPUT:
out.align the out.gaps file interspersed with the alignments
of the gaps.
out.errorsgaps the out.gaps file with an extra column stating the
number of errors contained in each gap.
out.gaps an ordered (clustered) list of matches with position
information, and gap distances between each match.
out.out a list of all maximal unique matches between the two
input sequences ordered by their start position in the
second sequence.
###gaps
Description:
This program reads a list of unique matches between two strings and
outputs the longest consistent set of matches, followed by all the
other matches. Part of the MUMmer1.0 pipeline and the output of the
mummer program needs to be processed (to strip all non-match lines)
before it can be passed to this program.
USAGE:
gaps <seq1> [-r] < <matchlist>
<seq1> The first sequence file that the match list represents.
<matchlist> A simple list of matches and NO header lines or other
mumbo jumbo. The columns of the match list should be
start in the reference, start in the query, and length
of the match.
[-r] Simply puts the string "reverse" on the header of the
output so 'annotate' knows to reverse the second
sequence.
OUTPUT:
stdout an ordered set of the input matches, separated by headers.
The first set is the longest consistent set of matches and
the second set is all other matches.
Notes:
This program will eventually be rewritten to be interchangeable with
mgaps, so that it may be plugged into the nucmer or promer
pipelines.
###mapview
Description:
mapview is a utility program for displaying sequence alignments as
provided by MUMmer, nucmer or promer. This program takes the output
from these alignment routines and converts it to a FIG, PDF or PS
file for visual analysis. It can also break the output into multiple
files for easier viewing and printing. Please refer to
"docs/mapview.README" for a more detailed description and explination.
USAGE:
mapview [options] <coords file> [UTR coords] [CDS coords]
[options] type 'mapview -h' for a list of options.
<coords file> show-coords output file
[UTR coords] UTR coordinate file in GFF format
[CDS coords] CDS coordinate file in GFF format
OUTPUT:
Default output format is an xfig file, however this can be changed to
a postscript of PDF file with the -f option. See 'mapview -h' for a
list of available formatting options.
Notes:
The produce the coords file input, show-coords must be run with the
-r -l options. To reduce redundant matches in promer output, run
show-coords with the -k option. To generate output formats other than
xfig, the fig2dev utility must be available from the system path. For
very large reference genomes, FIG format may be the only option that
will allow the entire display to be stored in one file, as fig2dev has
problems if the output is too large.