ALLVERSUSALL(1e) EMBOSS Manual for Debian ALLVERSUSALL(1e)
NAME
allversusall - Sequence similarity data from all-versus-all comparison.
SYNOPSIS
allversusall -seqinpath dirlist [-matrix matrixf] [-gapopen float] [-gapextend float] -datoutdir outdir -logfile outfile
allversusall -help
DESCRIPTION
allversusall is a command line program from EMBOSS ("the European Molecular Biology Open Software Suite"). It is part of the
"Utils:Database creation" command group(s).
OPTIONS
Input section
-seqinpath dirlist
Default value: ./
-matrix matrixf
This option specifies the residue substitution matrix that is used for sequence comparison. Default value: EBLOSUM62
Required section
Additional section
-gapopen float
This option specifies the gap insertion penalty. The gap insertion penalty is the score taken away when a gap is created. The best
value depends on the choice of comparison matrix. The default value assumes you are using the EBLOSUM62 matrix for protein sequences,
and the EDNAFULL matrix for nucleotide sequences. Default value: 10
-gapextend float
This option specifies the gap extension penalty. The gap extension, penalty is added to the standard gap penalty for each base or
residue in the gap. This is how long gaps are penalized. Usually you will expect a few long gaps rather than many short gaps, so the
gap extension penalty should be lower than the gap penalty. An exception is where one or both sequences are single reads with possible
sequencing errors in which case you would expect many single base gaps. You can get this result by setting the gap open penalty to zero
(or very low) and using the gap extension penalty to control gap scoring. Default value: 0.5
Output section
-datoutdir outdir
This option specifies the location of sequence similarity data files (output). Default value: ./
-logfile outfile
This option specifies the name of ALLVERSUSALL log file (output). The log file contains messages about any errors arising while
ALLVERSUSALL ran. Default value: allversusall.log
BUGS
Bugs can be reported to the Debian Bug Tracking system (http://bugs.debian.org/emboss), or directly to the EMBOSS developers
(http://sourceforge.net/tracker/?group_id=93650&atid=605031).
SEE ALSO
allversusall is fully documented via the tfm(1) system.
AUTHOR
Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Wrote the script used to autogenerate this manual page.
COPYRIGHT
This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package. It can be redistributed under the same terms as
EMBOSS itself.
DOMALIGN 0.1.0+20100721 08/11/2010 ALLVERSUSALL(1e)