polydot compares all sequences in a set of sequences. It then draws a dotplot for each pair of sequences by marking where words (tuples) of a specified length have an exact match in both sequences and optionally reports all identical matches to feature files.

Here is a sample session with polydot:

% polydot globin.fasta -gtitle="Polydot of globin.fasta"

Mandatory qualifiers (bold if not always prompted):

[-sequences] (seqset)

File containing a sequence alignment.

-wordsize (integer)

Word size.

-graph (graph)

Graph type.

-outfile (outfile)

Output filename.

Optional qualifiers:

-[no]boxit (boolean)

Draw a box around each dotplot.

-dumpfeat (boolean)

Dump all matches as feature files.

-format (string)

Format in which to dump.

-ext (string)

Extension for feature file.

Advanced qualifiers:

-data (boolean)

Output the match data to a file instead of plotting it.

-gap (integer)

This specifies the size of the gap that is used to separate the individual dotplots in the display. The size is measured in residues, as displayed in the output.