- Modified column score and sum of pairs score to divide the correct number of columns or pairs by the number of columns or pairs in the query alignment rather than the reference alignment
1.10.0
-Added tip_to_tip_node_distance (alias: t2t_node_dist; t2t_nd) function to calculate the phylogenetic distance between two leaves in a phylogeny. Distance is measured in nodes between two leaves
1.9.0
- Added monophyly_check (alias: is_monophyletic) function to examine monophyly among a specified set of taxa
1.8.0
- Added hidden_paralogy_check (alias: clan_check) function to examine phylogenetic tree for issues of hidden paralogy
1.7.0
- Added nearest_neighbor_interchange (alias: nni) function to generate all NNI moves for a binary rooted phylogeny
1.6.0
- Added tip_to_tip_distance (alias: t2t_dist; t2t) function to calculate phylogenetic distance between two leaves in a phylogeny