BAD_Mutations Version 1.0

First complete release of BAD_Mutations!

1.0 - 2016-05-27

Added

• compile subcommand up and running
• Full-featured test dataset

Modified

• Sequences with ambiguous nucleotides (WRKYSMVBHDN) are removed prior to
  alignment with PASTA
• fetch subcommand now downloads data from Phytozome 11
• Raw HyPhy report output makes sense now

Removed

• Unused options --codon and --min-seqs.