dotmatcher displays a thresholded dotplot of two sequences.
Here is a sample session with dotmatcher:
% dotmatcher sw:hba_human sw:hbb_human
Mandatory qualifiers (bold if not always prompted):
Output the match data to a file instead of plotting it.
Display as data.
Window size over which to test threshold.
This is the scoring matrix file used when comparing sequences. By default, the file is EBLOSUM62 (for proteins) or EDNAFULL (for nucleic sequences). These files are in the data directory of the EMBOSS installation.