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.

BAD_Mutations Version 0.2

Bugfix release.

Modified

• PASTA dies when sequences have internal stop codons. Sequences with internal stop codons are skipped from alignment.
• PASTA output files are prepared for HyPhy input prior to being copied to the output directory. This ensures that the input files are valid by the FASTA and Newick formats.
• Colons in query sequence names are replaced by underscores

BAD_Mutations Version 0.1

Initial public release of BAD_Mutations.

Added or Completed

• Database fetching
• BLAST searching
• PASTA alignment
• HyPhy prediction
• User manuals with installation and usage instructions

Planned for v1.0

• Creating complete configuration file, and switching format
• Completing the compile subcommand