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Cladistic analysis -- Software

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View Resource PAL: Phylogenetic Analysis Library

Created by researchers at the Universities of Auckland (New Zealand) and Oxford (UK), PAL (Phylogenetic Analysis Library) is a Java library intended for use in molecular evolution and phylogenetics. PAL currently consists of thirteen packages with "ready-to-use objects" for reading/writing sequence alignments, distance matrices, and trees; substitution models for nucleotides and amino acids;...

http://iubio.bio.indiana.edu/soft/molbio/evolve/pal/pal.html