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Blixem - display multiple alignments against a reference sequence.
Usage: blixem [options] [<sequencefile>] <datafile> [X options]
<sequencefile> contains the reference sequence in FASTA format.
<datafile> is a GFF v3 file containing alignments and other features.
If <sequencefile> is omitted, <datafile> should contain the reference
sequence in FASTA format, below a comment line that reads ##FASTA.
Both <sequencefile> and <datafile> can be substituted by "-"
for reading from stdin (pipe). If <sequencefile> is piped, the first
line should contain the sequence name and the second the sequence itself.
Options:
-t <type>, --display-type=<type> MANDATORY
Whether to display sequences in nucleotide or protein mode. Must be one of:
N = nucleotide
P = protein
-a <names>, --alignment-names=<names>
Specify a string giving the names of the alignments, e.g. "EST_mouse EST_human" etc.
-c <file>, --config-file=<file>
Read configuration options from 'file'.
--compiled
Show package compile date.
--dataset
Optional string to indicate a data-set that the alignments are from.
--dotter-first-match
Call Dotter on the first match to the right of the default start coord.
--fetch-server <nodeid:port>
Causes Blixem to get sequences from a fetch server at machine 'nodeid' on the given
port (default 22100).
-h, --help
More detailed usage information.
--hide-big-picture
Hide the big picture section on start-up.
--hide-inactive-strand
Hide the inactive strand (i.e. the reverse strand, or the forward strand if the -R option
is used).
--highlight-diffs
Enable 'highlight differences' mode, where mismatches (rather than matches) are highlighted.
--invert-sort
Invert sorting order
-m <from[:to]>, --map-coords=<from[:to]>
Map the coordinate system so that the given 'from' coordinate maps to the given
'to' coordinate (or to '1' if 'to' is not given).
-n, --negate-coords
When showing the reverse strand, negate the display coordinates.
-o <n>, --offset=<n>
Offset the reference sequence coordinate system by n.
--optional-data
Parse additional data such as organism and tissue-type on start-up.
--remove-input-files
Delete the input files after they have been parsed.
-r, --reverse-strand
Indicates that the given reference sequence is the reverse strand.
--save-temp-files
Save any temporary files created by Blixem.
--show-coverage
Display the coverage section on start-up.
--sort-mode=<mode>
Default sort mode. Use --help option to see details.
--squash-matches
Compress the alignment lists on start-up.
-s <n>, --start-coord=<n>
Start with the display centred on coordinate n.
--start-next-match
Start with the display centred on the first match to the right of the default start coord.
--styles-file=<file>
Read color options from a key-value file. Use --help option to see details.
--version
Show package version number.
-z <start:end>, --zoom-range=<start:end>
Specify the initial range of coordinates to zoom the big picture in to.
--zoom-whole
Start with the big picture zoomed out to view the full reference sequence range.
Some X options:
-acefont <font> Main font.
-font <font> Menu font.
-----
Written by Gemma Barson <gb10@sanger.ac.uk>
Based on original code by Erik Sonnhammer <Erik.Sonnhammer@sbc.su.se>
Reference: Sonnhammer ELL & Durbin R (1994). A workbench for Large Scale
Sequence Homology Analysis. Comput. Applic. Biosci. 10:301-307.
See http://www.sanger.ac.uk/resources/software/seqtools/ for more info.
Copyright (c) 2009-2011: Genome Research Ltd.
Blixem is distributed under the GNU General Public License; see http://www.gnu.org/copyleft/gpl.txt
Version 4.10-1-g6bff 17:38:25 Apr 4 2012
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