NAME

       blixem - 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.

blixem 4.44.1                                     October 2017                                         BLIXEM(1)