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jbloomlab / phydms

phylogenetic analyses informed by deep mutational scanning data
GNU General Public License v3.0
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Rel names #32

Closed skhilton closed 4 years ago

skhilton commented 4 years ago

This PR changes some of the command line interface names and slightly changes the output files.

@jon-mah: The purpose of this was to clean-up the code and make sure the naming was consistent. Can you look over the code and point out to me places I might have missed?