debian man page for dotter

DOTTER:(1)						      General Commands Manual							DOTTER:(1)

NAME
       dotter - Sequence dotplots with image enhancement tools.

SYNOPSIS
       dotter [options] <horizontal_sequence> <vertical_sequence> [X options]

DESCRIPTION
	      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.

       Allowed types:
	      Protein	     -	    Protein DNA 	   -	  DNA DNA	     -	    Protein

	      Options:

       -b <file>
	      Batch mode, write dotplot to <file>

       -l <file>
	      Load dotplot from <file>

       -m <float>
	      Memory usage limit in Mb (default 0.5)

       -z <int>
	      Set zoom (compression) factor

       -p <int>
	      Set pixel factor manually (ratio pixelvalue/score)

       -W <int>
	      Set sliding window size. (K => Karlin/Altschul estimate)

       -M <file>
	      Read in score matrix from <file> (Blast format; Default: Blosum62).

       -F <file>
	      Read in sequences and data from <file> (replaces sequencefiles).

       -f <file>
	      Read feature segments from <file>

       -H     Do not calculate dotplot at startup.

       -R     Reversed Greyramp tool at start.

       -r     Reverse and complement horizontal_sequence (DNA vs Protein)

       -D     Don't display mirror image in self comparisons

       -w     For DNA: horizontal_sequence top strand only (Watson)

       -c     For DNA: horizontal_sequence bottom strand only (Crick)

       -q <int>
	      Horizontal_sequence offset

       -s <int>
	      Vertical_sequence offset

	      Some X options: -acefont <font> Main font.  -font    <font> Menu font.

SEE ALSO
       http://www.cgb.ki.se/cgb/groups/sonnhammer/Dotter.html for more info.

AUTHOR
       Erik.Sonnhammer@cgb.ki.se Version 3.1, compiled Jul 10 2010

								     July 2010								DOTTER:(1)