File format converters. Mostly self-evident from the script name...
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fasta_to_phy.pl -- Convert a fasta file (aligned hopefully!) to (relaxed) phylip format.
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MFAtoPHY.pl -- a handy script from Yu-Wei Wu to convert a fasta file to a phylip file.
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nex_to_fasta.py -- A simple converter from Nexus to Fasta format using BioPython.
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nex_to_phy.py -- A simple converter from Nexus to relaxed-Phylip format using BioPython.