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.