.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
.TH BLIXEM "1" "October 2017" "blixem 4.44.1" "User Commands"
.SH NAME
blixem \- display multiple alignments against a reference sequence
.SH DESCRIPTION
.IP
Blixem \- display multiple alignments against a reference sequence.
.IP
Usage: blixem [options] [<sequence_file>] <data_file> [X options]
.IP
<sequence_file> contains the reference sequence in FASTA format.
<data_file> is a GFF v3 file containing alignments and other features.
If <sequence_file> is omitted, <data_file> should contain the reference
sequence in FASTA format, below a comment line that reads ##FASTA.
.IP
Both <sequence_file> and <data_file> can be substituted by "\-"
for reading from stdin (pipe).  If <sequence_file> is piped, the first
line should contain the sequence name and the second the sequence itself.
.IP
Options:
.TP
\fB\-t\fR <type>, \fB\-\-display\-type=\fR<type>
MANDATORY
.IP
Whether to display sequences in nucleotide or protein mode. Must be one of:
.IP
N = nucleotide
P = protein
.HP
\fB\-a\fR <names>, \fB\-\-alignment\-names=\fR<names>
.IP
Specify a string giving the names of the alignments, e.g. "EST_mouse EST_human" etc.
.HP
\fB\-c\fR <file>, \fB\-\-config\-file=\fR<file>
.IP
Read configuration options from 'file'.
.HP
\fB\-\-abbrev\-title\-on\fR
.IP
Abbreviate window title prefixes
.HP
\fB\-\-abbrev\-title\-off\fR
.IP
Do not abbreviate window title prefixes
.HP
\fB\-\-compiled\fR
.IP
Show package compile date.
.HP
\fB\-d\fR <data_file>, \fB\-\-data\-file=\fR<data_file>
.IP
Alternative way of specifying <data_file> using an argument
.HP
\fB\-\-dataset\fR
.IP
Optional string to indicate a data\-set that the alignments are from.
.HP
\fB\-e\fR <sequence_file>, \fB\-\-sequence\-file=\fR<sequence_file>
.IP
Alternative way of specifying <sequence_file> using an argument
.HP
\fB\-\-dotter\-first\-match\fR
.IP
Call Dotter on the first match to the right of the default start coord.
.HP
\fB\-\-fetch\-server\fR <nodeid:port>
.IP
Causes Blixem to get sequences from a fetch server at machine 'nodeid' on the given
port (default 22100).
.HP
\fB\-h\fR, \fB\-\-help\fR
.IP
More detailed usage information.
.HP
\fB\-\-hide\-big\-picture\fR
.IP
Hide the big picture section on start\-up.
.HP
\fB\-\-hide\-inactive\-strand\fR
.IP
Hide the inactive strand (i.e. the reverse strand, or the forward strand if the \fB\-R\fR option
is used).
.HP
\fB\-\-highlight\-diffs\fR
.IP
Enable 'highlight differences' mode, where mismatches (rather than matches) are highlighted.
.HP
\fB\-\-invert\-sort\fR
.IP
Invert sorting order
.HP
\fB\-m\fR <from[:to]>, \fB\-\-map\-coords=\fR<from[:to]>
.IP
Map the coordinate system so that the given 'from' coordinate maps to the given
\&'to' coordinate (or to '1' if 'to' is not given).
.HP
\fB\-n\fR, \fB\-\-negate\-coords\fR
.IP
When showing the reverse strand, negate the display coordinates.
.HP
\fB\-o\fR <n>, \fB\-\-offset=\fR<n>
.IP
Offset the reference sequence coordinate system by n.
.HP
\fB\-\-optional\-data\fR
.IP
Parse additional data such as organism and tissue\-type on start\-up.
.HP
\fB\-\-remove\-input\-files\fR
.IP
Delete the input files after they have been parsed.
.HP
\fB\-r\fR, \fB\-\-reverse\-strand\fR
.IP
Indicates that the given reference sequence is the reverse strand.
.HP
\fB\-\-save\-temp\-files\fR
.IP
Save any temporary files created by Blixem.
.HP
\fB\-\-show\-coverage\fR
.IP
Display the coverage section on start\-up.
.HP
\fB\-\-sort\-mode=\fR<mode>
.IP
Default sort mode. Use \fB\-\-help\fR option to see details.
.HP
\fB\-\-squash\-matches\fR
.IP
Compress the alignment lists on start\-up.
.HP
\fB\-s\fR <n>, \fB\-\-start\-coord=\fR<n>
.IP
Start with the display centred on coordinate n.
.HP
\fB\-\-start\-next\-match\fR
.IP
Start with the display centred on the first match to the right of the default start coord.
.HP
\fB\-y\fR <file>, \fB\-\-styles\-file=\fR<file>
.IP
Read color options from a key\-value file. Use \fB\-\-help\fR option to see details.
.HP
\fB\-\-version\fR
.IP
Show package version number.
.HP
\fB\-z\fR <start:end>, \fB\-\-zoom\-range=\fR<start:end>
.IP
Specify the initial range of coordinates to zoom the big picture in to.
.HP
\fB\-\-zoom\-whole\fR
.IP
Start with the big picture zoomed out to view the full reference sequence range.
.IP
Some X options:
\fB\-acefont\fR <font> Main font.
\fB\-font\fR    <font> Menu font.
.PP
\fB\-\-\-\-\-\fR
.IP
Written by Gemma Barson <gb10@sanger.ac.uk>
Based on original code by Erik Sonnhammer <Erik.Sonnhammer@sbc.su.se>
.IP
Reference: Sonnhammer ELL & Durbin R (1994). A workbench for Large Scale
.IP
Sequence Homology Analysis. Comput. Applic. Biosci. 10:301\-307.
.IP
See http://www.sanger.ac.uk/resources/software/seqtools/ for more info.
.IP
Copyright (c) 2009\-2015: Genome Research Ltd.
Blixem is distributed under the GNU General Public License; see http://www.gnu.org/copyleft/gpl.txt
.TP
Version 4.44.1
14:27:56 Oct 19 2017
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.