'\" t
.\"     Title: INFOALIGN
.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
.\"      Date: 05/11/2012
.\"    Manual: EMBOSS Manual for Debian
.\"    Source: EMBOSS 6.4.0
.\"  Language: English
.\"
.TH "INFOALIGN" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
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.SH "NAME"
infoalign \- Display basic information about a multiple sequence alignment
.SH "SYNOPSIS"
.HP \w'\fBinfoalign\fR\ 'u
\fBinfoalign\fR \fB\-sequence\ \fR\fB\fIseqset\fR\fR [\fB\-matrix\ \fR\fB\fImatrix\fR\fR] [\fB\-refseq\ \fR\fB\fIstring\fR\fR] \fB\-plurality\ \fR\fB\fIfloat\fR\fR \fB\-identity\ \fR\fB\fIfloat\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-html\ \fR\fB\fIboolean\fR\fR] \fB\-only\ \fR\fB\fIboolean\fR\fR \fB\-heading\ \fR\fB\fIboolean\fR\fR \fB\-usa\ \fR\fB\fIboolean\fR\fR \fB\-name\ \fR\fB\fIboolean\fR\fR \fB\-seqlength\ \fR\fB\fIboolean\fR\fR \fB\-alignlength\ \fR\fB\fIboolean\fR\fR \fB\-gaps\ \fR\fB\fIboolean\fR\fR \fB\-gapcount\ \fR\fB\fIboolean\fR\fR \fB\-idcount\ \fR\fB\fIboolean\fR\fR \fB\-simcount\ \fR\fB\fIboolean\fR\fR \fB\-diffcount\ \fR\fB\fIboolean\fR\fR \fB\-change\ \fR\fB\fIboolean\fR\fR \fB\-weight\ \fR\fB\fIboolean\fR\fR \fB\-description\ \fR\fB\fIboolean\fR\fR
.HP \w'\fBinfoalign\fR\ 'u
\fBinfoalign\fR \fB\-help\fR
.SH "DESCRIPTION"
.PP
\fBinfoalign\fR
is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Alignment:Multiple,Data retrieval:Sequence data" command group(s)\&.
.SH "OPTIONS"
.SS "Input section"
.PP
\fB\-sequence\fR \fIseqset\fR
.RS 4
The sequence alignment to be displayed\&.
.RE
.PP
\fB\-matrix\fR \fImatrix\fR
.RS 4
This is the scoring matrix file used when comparing sequences\&. By default it is the file \*(AqEBLOSUM62\*(Aq (for proteins) or the file \*(AqEDNAFULL\*(Aq (for nucleic sequences)\&. These files are found in the \*(Aqdata\*(Aq directory of the EMBOSS installation\&.
.RE
.PP
\fB\-refseq\fR \fIstring\fR
.RS 4
If you give the number in the alignment or the name of a sequence, it will be taken to be the reference sequence\&. The reference sequence is the one against which all the other sequences are compared\&. If this is set to 0 then the consensus sequence will be used as the reference sequence\&. By default the consensus sequence is used as the reference sequence\&.
.RE
.SS "Advanced section"
.PP
\fB\-plurality\fR \fIfloat\fR
.RS 4
Set a cut\-off for the % of positive scoring matches below which there is no consensus\&. The default plurality is taken as 50% of the total weight of all the sequences in the alignment\&. Default value: 50\&.0
.RE
.PP
\fB\-identity\fR \fIfloat\fR
.RS 4
Provides the facility of setting the required number of identities at a position for it to give a consensus\&. Therefore, if this is set to 100% only columns of identities contribute to the consensus\&. Default value: 0\&.0
.RE
.SS "Output section"
.PP
\fB\-outfile\fR \fIoutfile\fR
.RS 4
If you enter the name of a file here then this program will write the sequence details into that file\&.
.RE
.PP
\fB\-html\fR \fIboolean\fR
.RS 4
Default value: N
.RE
.PP
\fB\-only\fR \fIboolean\fR
.RS 4
This is a way of shortening the command line if you only want a few things to be displayed\&. Instead of specifying: \*(Aq\-nohead \-nousa \-noname \-noalign \-nogaps \-nogapcount \-nosimcount \-noidcount \-nodiffcount \-noweight\*(Aq to get only the sequence length output, you can specify \*(Aq\-only \-seqlength\*(Aq Default value: N
.RE
.PP
\fB\-heading\fR \fIboolean\fR
.RS 4
Default value: @(!$(only))
.RE
.PP
\fB\-usa\fR \fIboolean\fR
.RS 4
Default value: @(!$(only))
.RE
.PP
\fB\-name\fR \fIboolean\fR
.RS 4
Default value: @(!$(only))
.RE
.PP
\fB\-seqlength\fR \fIboolean\fR
.RS 4
Default value: @(!$(only))
.RE
.PP
\fB\-alignlength\fR \fIboolean\fR
.RS 4
Default value: @(!$(only))
.RE
.PP
\fB\-gaps\fR \fIboolean\fR
.RS 4
Default value: @(!$(only))
.RE
.PP
\fB\-gapcount\fR \fIboolean\fR
.RS 4
Default value: @(!$(only))
.RE
.PP
\fB\-idcount\fR \fIboolean\fR
.RS 4
Default value: @(!$(only))
.RE
.PP
\fB\-simcount\fR \fIboolean\fR
.RS 4
Default value: @(!$(only))
.RE
.PP
\fB\-diffcount\fR \fIboolean\fR
.RS 4
Default value: @(!$(only))
.RE
.PP
\fB\-change\fR \fIboolean\fR
.RS 4
Default value: @(!$(only))
.RE
.PP
\fB\-weight\fR \fIboolean\fR
.RS 4
Default value: @(!$(only))
.RE
.PP
\fB\-description\fR \fIboolean\fR
.RS 4
Default value: @(!$(only))
.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
infoalign 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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