Change log


Major changes to PhyKIT are summarized here.

0.0.9: PhyKIT now handles error stemming from piping output

0.1.2: Added function (sum_of_pairs_score; sops; sop) to calculate the quality of an alignment given an input query alignment and a reference alignment to compare it to

0.1.3: Added function (column_score; cs) to calculate the quality of an alignment given an input query alignment and a reference alignment to compare it to

1.0.2: function that calculates Robinson Foulds distance (robinson_foulds_distance; rf_distance; rf_dist; rf) now can take trees that differ in topology. PhyKIT will first determine shared tips between the two trees and prune both trees to a common set of tips. Next, PhyKIT will calculate the Robinson Foulds distance.

1.0.3: added rooting procedure before calculating RF to handle comparing unrooted and rooted trees

1.1.0: added faidx (alias: get_entry; ge) function to extract fasta entries from a multi-fasta file

1.2.0: added command line interfaces for all functions so that each command can easily be executed. For example, ‘phykit aln_len -h’ can now be called using ‘pk_aln_len -h’