'\" t .\" Title: INFOALIGN .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" 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" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .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\&. .sp