NAME

       blixemh - 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

       -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

AUTHOR

       This manpage was written by Andreas Tille for the Debian distribution and can be used  for
       any other usage of the program.