'\" t
.\"     Title: SHOWALIGN
.\"    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 "SHOWALIGN" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
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.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\&.
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