---
name: "dotter"
section: "1"
platform: "linux"
package: "dotter"
version: "4.44.1+dfsg-7.1+b3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/dotter"
---

# dotter(1)

Sequence dotplots with image enhancement tools

## 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.