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 ommitted, <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 Public License; see http://www.gnu.org/copyleft/gpl.txt

 Version 4.10-1-g6bff  17:38:25 Apr  4 2012