Pontos

Pontos is an easy-to-use, graphical Java program for the calculation of uncorrected distance (or similarity) matrices from DNA sequence alignments in PHYLIP format. It also creates "difference" alignments from regular ones (and vice-versa).

It can handle gaps and ambiguities in different ways.

Gaps can be:
- all used;
- all ignored;
- ignored only at the ends of the sequences, in a pairwise manner;
- ignored only at the ends, but now globally (in effect trimming the whole alignment to the farthest sequences from the ends).

Ambiguities (things like R, Y, N, W, etc. in a DNA sequence) can be treated like:

- consider ambiguities as always different;
- consider ambiguity as partially different (e.g. R would be 0.5 different from A or G);
- ignore ambiguities in each pairwise comparison;
- remove all columns, globally, that show any ambiguity.

Pontos was written in Linux, but should run in any system where Java works. Pontos is licensed under the GPL version 3.