Pontos
Pontos calculates distance matrices from DNA sequence alignments.
... 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.