- calculations of pairwise identity in alignment now supports excluding pairwise combinations with gaps.
1.12.3
- hidden paralogy check now simply looks for monophyly or lack thereof for a set of taxa. Hidden paralogy check still reports insufficient taxon representation.
1.12.2
- removed root.txt file from DVMC function. User's are now recommended to trim outgroup taxa beforehand
1.11.3
- Added an optional argument to the prune_tree function wherein instead of pruning tips specified in the input file, those tips will be kept
1.11.1
- Modified sum of pairs score to divide the correct number of pairs by the number of pairs in the reference alignment rather than the query alignment alignment
1.11.0
- Added terminal_branch_stats (alias: tbs) function to examine terminal branch lengths