dotpath displays a non-overlapping wordmatch dotplot of two sequences. dotpath is very similar to the program dottup, which looks for places where words (tuples) of a specified length have an exact match in both sequences and draws a diagonal line over the position of those words.
Here is a sample session with dotpath:
% dotpath embl:AF129756 embl:AP000504 -word 20 Displays a non-overlapping wordmatch dotplot of two sequences Graph type [x11]:
Mandatory qualifiers (bold if not always prompted):