blixemh1

Overview

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

-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

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Written by Gemma Barson <[email protected]> Based on original code by Erik Sonnhammer <[email protected]>

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