blixem(1)
display multiple alignments against a reference sequence
Description
BLIXEM
NAME
blixem - display multiple alignments against a reference sequence
DESCRIPTION
Blixem - display multiple alignments against a reference sequence.
Usage: blixem [options] [<sequence_file>] <data_file> [X options]
<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.
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.
Options:
-t <type>, --display-type=<type>
MANDATORY
Whether to display sequences in nucleotide or protein mode. Must be one of:
N = nucleotide P = protein
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-a <names>, --alignment-names=<names> |
Specify a string giving the names of the alignments, e.g. "EST_mouse EST_human" etc.
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-c <file>, --config-file=<file> |
Read configuration options from ’file’.
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--abbrev-title-on |
Abbreviate window title prefixes
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--abbrev-title-off |
Do not abbreviate window title prefixes
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--compiled |
Show package compile date.
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-d <data_file>, --data-file=<data_file> |
Alternative way of specifying <data_file> using an argument
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--dataset |
Optional string to indicate a data-set that the alignments are from.
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-e <sequence_file>, --sequence-file=<sequence_file> |
Alternative way of specifying <sequence_file> using an argument
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--dotter-first-match |
Call Dotter on the first match to the right of the default start coord.
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--fetch-server <nodeid:port> |
Causes Blixem to get sequences from a fetch server at machine ’nodeid’ on the given port (default 22100).
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-h, --help |
More detailed usage information.
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--hide-big-picture |
Hide the big picture section on start-up.
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--hide-inactive-strand |
Hide the inactive strand (i.e. the reverse strand, or the forward strand if the -R option is used).
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--highlight-diffs |
Enable ’highlight differences’ mode, where mismatches (rather than matches) are highlighted.
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--invert-sort |
Invert sorting order
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-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).
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-n, --negate-coords |
When showing the reverse strand, negate the display coordinates.
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-o <n>, --offset=<n> |
Offset the reference sequence coordinate system by n.
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--optional-data |
Parse additional data such as organism and tissue-type on start-up.
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--remove-input-files |
Delete the input files after they have been parsed.
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-r, --reverse-strand |
Indicates that the given reference sequence is the reverse strand.
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--save-temp-files |
Save any temporary files created by Blixem.
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--show-coverage |
Display the coverage section on start-up.
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--sort-mode=<mode> |
Default sort mode. Use --help option to see details.
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--squash-matches |
Compress the alignment lists on start-up.
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-s <n>, --start-coord=<n> |
Start with the display centred on coordinate n.
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--start-next-match |
Start with the display centred on the first match to the right of the default start coord.
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-y <file>, --styles-file=<file> |
Read color options from a key-value file. Use --help option to see details.
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--version |
Show package version number.
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-z <start:end>, --zoom-range=<start:end> |
Specify the initial range of coordinates to zoom the big picture in to.
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--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.
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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) 2009-2015: Genome Research Ltd. Blixem is distributed under the GNU General Public License; see http://www.gnu.org/copyleft/gpl.txt
Version 4.44.1
14:27:56 Oct 19 2017
AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.