Preamble
BuddySuite had been neglected for several years... Notably, BioPython has made some fundamental changes that really broke how Sequence objects were being handled, so BuddySuite has been essentially useless for quite some time. This release has a number of non-trivial issues, but at least the tools run again.
General
- Bash script provided to install all BuddySuite dependencies
- Smarter/faster format guessing
SeqBuddy
New functions
- head()
- tail()
Upgrades
- Change name split_by_seq_number to split_by_x_seqs
- Change name split_by_file_number to split_by_x_files
- Major rewrite of PrositeScan (switch to InterProScan server)
- Performance enhancements to delete_records() and delete_repeats()
- Performance enhancements to bl2seq
AlignBuddy
Upgrades
- Performance enhancements to FeatureReMapper()
- Performance enhancements to percent_id()
- Allow positional information to be suppressed in concat_alignment()
- Implement len
PhyloBuddy
New Functions
- add_branch()
Upgrades
- Added IQ-Tree support
- Add support for FigTree
- Implement len
- Add support for RAxML majority rule consensus tree