supermatcher1e
Calculate approximate local pair-wise alignments of larger sequences
Usage
supermatcher -asequence
seqall
-bsequence
seqset
[-datafile
matrixf]
[-minscore
float]
-gapopen
float
-gapextend
float
[-width
integer]
[-wordlen
integer]
-outfile
align
[-errorfile
outfile]
supermatcher -help
Overview
supermatcher is a command line program from EMBOSS (“the European Molecular Biology Open Software Suite”). It is part of the "Alignment:Local" command group(s).
Options
Input section
-
-asequence seqall
-
-bsequence seqset
-
-datafile matrixf -
This is the scoring matrix file used when comparing sequences. By default it is the file 'EBLOSUM62' (for proteins) or the file 'EDNAFULL' (for nucleic sequences). These files are found in the 'data' directory of the EMBOSS installation.
-
-minscore float -
Minimum alignment score to report an alignment.
Required section
-
-gapopen float -
Default value: @($(acdprotein)? 10.0 : 10.0)
-
-gapextend float -
Default value: @($(acdprotein)? 0.5 : 0.5)
Additional section
-
-width integer -
Default value: 16
-
-wordlen integer -
Default value: 6
Output section
-
-outfile align
-
-errorfile outfile -
Error file to be written to for failed alignments Default value: supermatcher.error
Releases
9 releases since Debian 5.0 (Lenny); the text changed 2 times.
-minscore since Debian 7 (Wheezy).