blixem - display multiple alignments against a reference
sequence
- 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
-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'.
--abbrev-title-on
- Abbreviate window title prefixes
--abbrev-title-off
- Do not abbreviate window title prefixes
--compiled
- Show package compile date.
-d <data_file>,
--data-file=<data_file>
- Alternative way of specifying <data_file> using an argument
--dataset
- Optional string to indicate a data-set that the alignments are from.
-e <sequence_file>,
--sequence-file=<sequence_file>
- Alternative way of specifying <sequence_file> using an argument
--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.
-y <file>, --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) 2009-2015: 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
This manpage was written by Andreas Tille for the Debian
distribution and can be used for any other usage of the program.