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.
Be the first to post a review of Pontos!