DOTTER:(1)

NAME

dotter - Sequence dotplots with image enhancement tools.

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

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 Pro: tein)
-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.