.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
.TH DOTTER "1" "October 2017" "dotter 4.44.1" "User Commands"
.SH NAME
dotter \- Sequence dotplots with image enhancement tools
.SH DESCRIPTION
.IP
Dotter \- Sequence dotplots with image enhancement tools.
.TP
Usage: dotter [options] <horizontal_sequence> <vertical_sequence>
[X options]
.IP
Where <horizontal_sequence> and <vertical_sequence> are file names for FASTA files
containing the two sequences.
.TP
Allowed sequence types:
Protein  \-   Protein
DNA      \-   DNA
DNA      \-   Protein
.IP
Options:
.HP
\fB\-h\fR, \fB\-\-help\fR
.IP
Show this usage information
.HP
\fB\-b\fR <file>, \fB\-\-batch\-save=\fR<file>
.IP
Batch mode; save dot matrix to <file>
.HP
\fB\-e\fR <file>, \fB\-\-batch\-export=\fR<file>
.IP
Batch mode; export plot to PDF file <file>
.HP
\fB\-l\fR <file>, \fB\-\-load\fR
.IP
Load dot matrix from <file>
.HP
\fB\-m\fR <float>, \fB\-\-memory\-limit=\fR<float>
.IP
Memory usage limit in Mb (default 0.5)
.HP
\fB\-z\fR <int>, \fB\-\-zoom\fR
.IP
Set zoom (compression) factor
.HP
\fB\-p\fR <int>, \fB\-\-pixel\-factor\fR
.IP
Set pixel factor manually (ratio pixelvalue/score)
.HP
\fB\-W\fR <int>, \fB\-\-window\-size\fR
.IP
Set sliding window size. (K => Karlin/Altschul estimate)
.HP
\fB\-M\fR <file>, \fB\-\-matrix\-file=\fR<file>
.IP
Read in score matrix from <file> (Blast format; Default: Blosum62).
.HP
\fB\-F\fR <file>, \fB\-\-sequence\-file\fR
.IP
Read in sequences and data from <file> (replaces sequencefiles).
.HP
\fB\-f\fR <file>, \fB\-\-feature\-file\fR
.IP
Read feature segments from <file>
.HP
\fB\-H\fR, \fB\-\-hsp\-mode\fR
.IP
Do not calculate dotplot at startup.
.HP
\fB\-R\fR, \fB\-\-reverse\-greyramp\fR
.IP
Reversed Greyramp tool at start.
.HP
\fB\-r\fR, \fB\-\-reverse\-horizontal\fR
.IP
Reverse and complement horizontal_sequence (if DNA)
.HP
\fB\-v\fR, \fB\-\-reverse\-vertical\fR
.IP
Reverse and complement vertical_sequence (if DNA)
.HP
\fB\-D\fR, \fB\-\-disable\-mirror\fR
.IP
Don't display mirror image in self comparisons
.HP
\fB\-w\fR, \fB\-\-watson\-only\fR
.IP
For DNA: horizontal_sequence top strand only (Watson)
.HP
\fB\-c\fR, \fB\-\-crick\-only\fR
.IP
For DNA: horizontal_sequence bottom strand only (Crick)
.HP
\fB\-q\fR <int>, \fB\-\-horizontal\-offset=\fR<int>
.IP
Horizontal_sequence offset
.HP
\fB\-s\fR <int>, \fB\-\-vertical\-offset=\fR<int>
.IP
Vertical_sequence offset
.HP
\fB\-\-horizontal\-type\fR=\fI\,p\/\fR|d
.IP
Horizontal_sequence type ('p' for peptide or 'd' for DNA)
.HP
\fB\-\-vertical\-type\fR=\fI\,p\/\fR|d
.IP
Vertical_sequence type ('p' for peptide or 'd' for DNA)
.HP
\fB\-\-abbrev\-title\-on\fR
.IP
Abbreviate window title prefixes
.HP
\fB\-\-abbrev\-title\-off\fR
.IP
Do not abbreviate window title prefixes
.HP
\fB\-\-session_colour=\fR<colour_str>
.IP
Set the background colour of the dotter window
.HP
\fB\-\-compiled\fR
.IP
Show package compile date
.HP
\fB\-\-version\fR
.IP
Show package version
.PP
\fB\-\-\-\-\-\fR
.IP
Written by Gemma Barson <gb10@sanger.ac.uk>
Based on original code by Erik Sonnhammer <Erik.Sonnhammer@sbc.su.se>
.IP
Reference: Sonnhammer ELL & Durbin R (1995). A dot\-matrix program
.IP
with dynamic threshold control suited for genomic DNA and protein
sequence analysis. Gene 167(2):GC1\-10.
.IP
See http://www.sanger.ac.uk/resources/software/seqtools/ for more info.
.IP
Copyright (c) 2010\-2015: Genome Research Ltd.
Dotter is distributed under the GNU General Public License; see http://www.gnu.org/copyleft/gpl.txt
.TP
Version 4.44.1
14:27:56 Oct 19 2017
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.