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.