'\" t .\" Title: SHOWALIGN .\" 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 "SHOWALIGN" "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" showalign \- Display a multiple sequence alignment in pretty format .SH "SYNOPSIS" .HP \w'\fBshowalign\fR\ 'u \fBshowalign\fR \fB\-sequence\ \fR\fB\fIseqset\fR\fR [\fB\-matrix\ \fR\fB\fImatrix\fR\fR] [\fB\-refseq\ \fR\fB\fIstring\fR\fR] [\fB\-bottom\ \fR\fB\fIboolean\fR\fR] [\fB\-show\ \fR\fB\fIlist\fR\fR] [\fB\-order\ \fR\fB\fIlist\fR\fR] [\fB\-similarcase\ \fR\fB\fIboolean\fR\fR] [\fB\-consensus\ \fR\fB\fIboolean\fR\fR] \fB\-uppercase\ \fR\fB\fIrange\fR\fR \fB\-number\ \fR\fB\fIboolean\fR\fR \fB\-ruler\ \fR\fB\fIboolean\fR\fR \fB\-width\ \fR\fB\fIinteger\fR\fR \fB\-margin\ \fR\fB\fIinteger\fR\fR \fB\-html\ \fR\fB\fIboolean\fR\fR \fB\-highlight\ \fR\fB\fIrange\fR\fR \fB\-plurality\ \fR\fB\fIfloat\fR\fR \fB\-setcase\ \fR\fB\fIfloat\fR\fR \fB\-identity\ \fR\fB\fIfloat\fR\fR \fB\-gaps\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBshowalign\fR\ 'u \fBshowalign\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBshowalign\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 .SS "Additional section" .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 always shown in full and 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 .PP \fB\-bottom\fR \fIboolean\fR .RS 4 If this is true then the reference sequence is displayed at the bottom of the alignment instead of the top\&. Default value: Y .RE .PP \fB\-show\fR \fIlist\fR .RS 4 Default value: N .RE .PP \fB\-order\fR \fIlist\fR .RS 4 Default value: I .RE .PP \fB\-similarcase\fR \fIboolean\fR .RS 4 If this is set True, then when \-show is set to \*(AqSimilarities\*(Aq or \*(AqNon\-identities\*(Aq and a residue is similar but not identical to the reference sequence residue, it will be changed to lower\-case\&. If \-show is set to \*(AqAll\*(Aq then non\-identical, non\-similar residues will be changed to lower\-case\&. If this is False then no change to the case of the residues is made on the basis of their similarity to the reference sequence\&. Default value: Y .RE .PP \fB\-consensus\fR \fIboolean\fR .RS 4 If this is true then the consensus line is displayed\&. Default value: Y .RE .SS "Advanced section" .PP \fB\-uppercase\fR \fIrange\fR .RS 4 Regions to put in uppercase\&. If this is left blank, then the sequence case is left alone\&. A set of regions is specified by a set of pairs of positions\&. The positions are integers\&. They are separated by any non\-digit, non\-alpha character\&. Examples of region specifications are: 24\-45, 56\-78 1:45, 67=99;765\&.\&.888 1,5,8,10,23,45,57,99 .RE .PP \fB\-number\fR \fIboolean\fR .RS 4 If this option is true then a line giving the positions in the alignment is displayed every 10 characters above the alignment\&. Default value: Y .RE .PP \fB\-ruler\fR \fIboolean\fR .RS 4 If this option is true then a ruler line marking every 5th and 10th character in the alignment is displayed\&. Default value: Y .RE .PP \fB\-width\fR \fIinteger\fR .RS 4 Default value: 60 .RE .PP \fB\-margin\fR \fIinteger\fR .RS 4 This sets the length of the left\-hand margin for sequence names\&. If the margin is set at 0 then no margin and no names are displayed\&. If the margin is set to a value that is less than the length of a sequence name then the sequence name is displayed truncated to the length of the margin\&. If the margin is set to \-1 then the minimum margin width that will allow all the sequence names to be displayed in full plus a space at the end of the name will automatically be selected\&. Default value: \-1 .RE .PP \fB\-html\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-highlight\fR \fIrange\fR .RS 4 Regions to colour if formatting for HTML\&. If this is left blank, then the sequence is left alone\&. A set of regions is specified by a set of pairs of positions\&. The positions are integers\&. They are followed by any valid HTML font colour\&. Examples of region specifications are: 24\-45 blue 56\-78 orange 1\-100 green 120\-156 red A file of ranges to colour (one range per line) can be specified as \*(Aq@filename\*(Aq\&. .RE .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\-setcase\fR \fIfloat\fR .RS 4 Sets the threshold for the scores of the positive matches above which the consensus is in upper\-case and below which the consensus is in lower\-case\&. By default this is set to be half of the (weight\-adjusted) number of sequences in the alignment\&. Default value: @( $(sequence\&.totweight) / 2) .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 .PP \fB\-gaps\fR \fIboolean\fR .RS 4 If this option is true then gap characters can appear in the consensus\&. The alternative is \*(AqN\*(Aq for nucleotide, or \*(AqX\*(Aq for protein Default value: Y .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .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 showalign 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