.\" This file was generated by help2man 1.37.1 and then manually edited.
.TH DOTTER: "1" "July 2010" 
.SH NAME
dotter \- Sequence dotplots with image enhancement tools.
.SH SYNOPSIS
dotter [options] <horizontal_sequence> <vertical_sequence> [X options]
.SH DESCRIPTION
.IP
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.
.TP
.TP
Allowed types:
Protein        \-      Protein
DNA            \-      DNA
DNA            \-      Protein
.IP
Options:
.TP
\fB\-b\fR <file>
Batch mode, write dotplot to <file>
.TP
\fB\-l\fR <file>
Load dotplot from <file>
.TP
\fB\-m\fR <float>
Memory usage limit in Mb (default 0.5)
.TP
\fB\-z\fR <int>
Set zoom (compression) factor
.TP
\fB\-p\fR <int>
Set pixel factor manually (ratio pixelvalue/score)
.TP
\fB\-W\fR <int>
Set sliding window size. (K => Karlin/Altschul estimate)
.TP
\fB\-M\fR <file>
Read in score matrix from <file> (Blast format; Default: Blosum62).
.TP
\fB\-F\fR <file>
Read in sequences and data from <file> (replaces sequencefiles).
.TP
\fB\-f\fR <file>
Read feature segments from <file>
.TP
\fB\-H\fR
Do not calculate dotplot at startup.
.TP
\fB\-R\fR
Reversed Greyramp tool at start.
.TP
\fB\-r\fR
Reverse and complement horizontal_sequence (DNA vs Protein)
.TP
\fB\-D\fR
Don't display mirror image in self comparisons
.TP
\fB\-w\fR
For DNA: horizontal_sequence top strand only (Watson)
.TP
\fB\-c\fR
For DNA: horizontal_sequence bottom strand only (Crick)
.TP
\fB\-q\fR <int>
Horizontal_sequence offset
.TP
\fB\-s\fR <int>
Vertical_sequence offset
.IP
Some X options:
\fB\-acefont\fR <font> Main font.
\fB\-font\fR    <font> Menu font.
.SH SEE ALSO
http://www.cgb.ki.se/cgb/groups/sonnhammer/Dotter.html for more info.
.SH AUTHOR
Erik.Sonnhammer@cgb.ki.se
Version 3.1, compiled Jul 10 2010