'\" t
.\"     Title: ALLVERSUSALL
.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.75.2 <http://docbook.sf.net/>
.\"      Date: 08/11/2010
.\"    Manual: EMBOSS Manual for Debian
.\"    Source: DOMALIGN 0.1.0+20100721
.\"  Language: English
.\"
.TH "ALLVERSUSALL" "1e" "08/11/2010" "DOMALIGN 0.1.0+20100721" "EMBOSS Manual for Debian"
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.SH "NAME"
allversusall \- Sequence similarity data from all\-versus\-all comparison\&.
.SH "SYNOPSIS"
.HP \w'\fBallversusall\fR\ 'u
\fBallversusall\fR \fB\-seqinpath\ \fR\fB\fIdirlist\fR\fR [\fB\-matrix\ \fR\fB\fImatrixf\fR\fR] [\fB\-gapopen\ \fR\fB\fIfloat\fR\fR] [\fB\-gapextend\ \fR\fB\fIfloat\fR\fR] \fB\-datoutdir\ \fR\fB\fIoutdir\fR\fR \fB\-logfile\ \fR\fB\fIoutfile\fR\fR
.HP \w'\fBallversusall\fR\ 'u
\fBallversusall\fR \fB\-help\fR
.SH "DESCRIPTION"
.PP
\fBallversusall\fR
is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database creation" command group(s)\&.
.SH "OPTIONS"
.SS "Input section"
.PP
\fB\-seqinpath\fR \fIdirlist\fR
.RS 4
Default value: \&./
.RE
.PP
\fB\-matrix\fR \fImatrixf\fR
.RS 4
This option specifies the residue substitution matrix that is used for sequence comparison\&. Default value: EBLOSUM62
.RE
.SS "Required section"
.SS "Additional section"
.PP
\fB\-gapopen\fR \fIfloat\fR
.RS 4
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
.RE
.PP
\fB\-gapextend\fR \fIfloat\fR
.RS 4
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
.RE
.SS "Output section"
.PP
\fB\-datoutdir\fR \fIoutdir\fR
.RS 4
This option specifies the location of sequence similarity data files (output)\&. Default value: \&./
.RE
.PP
\fB\-logfile\fR \fIoutfile\fR
.RS 4
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
.RE
.SH "BUGS"
.PP
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)\&.
.SH "SEE ALSO"
.PP
allversusall is fully documented via the
\fBtfm\fR(1)
system\&.
.SH "AUTHOR"
.PP
\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
.RS 4
Wrote the script used to autogenerate this manual page\&.
.RE
.SH "COPYRIGHT"
.br
.PP
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\&.
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