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.