NAME

       dotter - Sequence dotplots with image enhancement tools

DESCRIPTION

              Dotter - Sequence dotplots with image enhancement tools.

       Usage: dotter [options] <horizontal_sequence> <vertical_sequence>
              [X options]

              Where  <horizontal_sequence> and <vertical_sequence> are file names for FASTA files containing the
              two sequences.

       Allowed sequence types:
              Protein  -   Protein DNA      -   DNA DNA      -   Protein

              Options:

       -h, --help

              Show this usage information

       -b <file>, --batch-save=<file>

              Batch mode; save dot matrix to <file>

       -e <file>, --batch-export=<file>

              Batch mode; export plot to PDF file <file>

       -l <file>, --load

              Load dot matrix from <file>

       -m <float>, --memory-limit=<float>

              Memory usage limit in Mb (default 0.5)

       -z <int>, --zoom

              Set zoom (compression) factor

       -p <int>, --pixel-factor

              Set pixel factor manually (ratio pixelvalue/score)

       -W <int>, --window-size

              Set sliding window size. (K => Karlin/Altschul estimate)

       -M <file>, --matrix-file=<file>

              Read in score matrix from <file> (Blast format; Default: Blosum62).

       -F <file>, --sequence-file

              Read in sequences and data from <file> (replaces sequencefiles).

       -f <file>, --feature-file

              Read feature segments from <file>

       -H, --hsp-mode

              Do not calculate dotplot at startup.

       -R, --reverse-greyramp

              Reversed Greyramp tool at start.

       -r, --reverse-horizontal

              Reverse and complement horizontal_sequence (if DNA)

       -v, --reverse-vertical

              Reverse and complement vertical_sequence (if DNA)

       -D, --disable-mirror

              Don't display mirror image in self comparisons

       -w, --watson-only

              For DNA: horizontal_sequence top strand only (Watson)

       -c, --crick-only

              For DNA: horizontal_sequence bottom strand only (Crick)

       -q <int>, --horizontal-offset=<int>

              Horizontal_sequence offset

       -s <int>, --vertical-offset=<int>

              Vertical_sequence offset

       --horizontal-type=p|d

              Horizontal_sequence type ('p' for peptide or 'd' for DNA)

       --vertical-type=p|d

              Vertical_sequence type ('p' for peptide or 'd' for DNA)

       --abbrev-title-on

              Abbreviate window title prefixes

       --abbrev-title-off

              Do not abbreviate window title prefixes

       --session_colour=<colour_str>

              Set the background colour of the dotter window

       --compiled

              Show package compile date

       --version

              Show package version

       -----

              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 (1995). A dot-matrix program

              with  dynamic  threshold  control  suited  for  genomic  DNA  and  protein sequence analysis. Gene
              167(2):GC1-10.

              See http://www.sanger.ac.uk/resources/software/seqtools/ for more info.

              Copyright (c) 2010-2015: Genome Research Ltd.  Dotter 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.

dotter 4.44.1                                     October 2017                                         DOTTER(1)