 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.

  -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.


FEATURES
  The preferred file format for <datafile> is GFF v3. (However, Blixem is still compatible with
  older file formats such as exblx and seqbl, as used by MSPcrunch).

  Blixem is mainly aimed at displaying alignments, but can also show other features such as
  transcripts, variations and polyA tails. The supported SO terms are:
    match
    nucleotide_match
    protein_match
    match_part
    match_set
    transcript
    primary_transcript
    processed_transcript
    mRNA
    CDS
    UTR
    exon
    intron
    SNP
    copy_number_variation
    substitution
    insertion
    deletion
    sequence_alteration
    polyA_signal_sequence
    polyA_site
    read
    region

SORT MODE
  The sort mode is specified with the --sort-mode=<mode> argument, where <mode> is
  one of the following:
    s = by Score
    i = by Identity
    n = by Name
    p = by Position

  If optional data is loaded on start-up using the --optional-data argument, then the following
  sort modes are also valid:
    t = by Tissue type
    m = by Strain
    g = by Gene name
    o = by Organism

COLOR KEY FILE
  The color key file is specified with the -y <file> or --styles-file=<file> argument. This is a .ini-
  like file that specifies attributes such as fill and line colors for features from particular 
  sources (say EST_Human or polya_signal). The file should contain one or more source stanzas followed
  by one or more key=value pairs, i.e. 

    [<source>]
      <key>=<value>
      ...

  <key> can be one of:
      colours:                 default colours
      transcript-cds-colours:  used to specify a different colour 
                               for CDS sections of transcripts

  <value> is a semi-colon separated list of fill and line colours of the format:
      <normal|selected> <fill|border> <colour>

  <colour> can be in any of the forms accepted by XParseColor; these include name 
           for a colour from rgb.txt, such as DarkSlateGray, or a hex specification 
           such as #305050.

  Example:
    colours=normal border #0000af ; selected border #0000af ; normal fill white ; \
            selected fill #ffddcc ; 
    transcript-cds-colours=normal border #0000af ; selected border #0000af ; \
            normal fill white ; selected fill #ffddcc ; 

  Note that selection colors will be calculated automatically if they are not
  specified (a darker shade of the default color will be used when the feature is selected).

MSPcrunch
  To make the datafile from blast output, run MSPcrunch with option -q.

 o To pipe MSPcrunch output directly to Blixem, use "-"
   as the second parameter ([datafile]).  Example:

   MSPcrunch -q <my.blast_output> | blixem <my.seq> -

 o The BLAST program (blastp, blastn, blastx, tblastn, tblastx)
   is automatically detected from the Blast output header by MSPcrunch
   and is passed on to Blixem in the seqbl format (-q).

-----
 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
