Updates to BAD_Mutations will be documented here. Versioning follows the form X.Y, where X is the major version, and Y is the minor version. Major version increments involve alterations to the way the user interacts with the program, or fundamentally change how the program behaves. Examples are switching of supported file formats or addition of new subcommands. Minor version increments are small feature additions or bug fixes. Examples are modifications to existing subcommands or alterations to output file formats. Modifications to documentation do not alter version numbers.
compilesubcommand up and running- Full-featured test dataset
- Sequences with ambiguous nucleotides (WRKYSMVBHDN) are removed prior to alignment with PASTA
fetchsubcommand now downloads data from Phytozome 11- Raw HyPhy report output makes sense now
- Unused options
--codonand--min-seqs.
- Sequences with internal stop codons are skipped from PASTA alignment
- Colons(:) are replaced by underscores(_) in alignment and prediction
- MSA and phylogenetic trees are cleaned for HyPhy input prior to being copied to the output directory
- User manuals in plain text and GitHub-Flavored Markdown
- Brief section on parallel processing to the manual
- This CHANGELOG to document changes
- Old workflows
- Old package source files