Pontos Wiki
Pontos calculates distance matrices from DNA sequence alignments.
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After downloading and "installing" Pontos (as described in [How to install]), running the program is very easy: double click on the JAR file (or the launcher, if you created one) and the program's interface should appear (click below for larger version).
The interface is simple, and each area is responsible for the setting of a different type of option for the handling of uncorrected distance calculations.