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DOTTER(1) User Commands DOTTER(1)


dotter - Sequence dotplots with image enhancement tools


Dotter - Sequence dotplots with image enhancement tools.
[X options]
Where <horizontal_sequence> and <vertical_sequence> are file names for FASTA files containing the two sequences.
Protein - Protein DNA - DNA DNA - Protein

-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_sequence type ('p' for peptide or 'd' for DNA)


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


Abbreviate window title prefixes


Do not abbreviate window title prefixes


Set the background colour of the dotter window


Show package compile date


Show package version


Written by Gemma Barson <> Based on original code by Erik Sonnhammer <>
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 for more info.
Copyright (c) 2010-2015: Genome Research Ltd. Dotter is distributed under the GNU General Public License; see
14:27:56 Oct 19 2017


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

October 2017 dotter 4.44.1