Python

phykit

Latest version: v1.11.14

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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

1.11.2

- Added an optional argument to the thread_dna function. Now, PhyKIT can thread nucleotide
sequences onto a trimmed amino acid alignment. To do so, point PhyKIT to the ClipKIT outputted log
file using the -c argument. The ClipKIT log file can be generated when trimming an alignment with
ClipKIT by adding the -l argument (see here for more details: https://jlsteenwyk.com/ClipKIT/).

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

1.10.1

- 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

1.5.0

- Added root_tree (alias: root; rt) function to root a phylogenetic tree

1.4.0

- PhyKIT is now Python version 3.9 and BioPython 1.79 compatible

1.3.0

- Added function that estimates the evolutionary rate of a gene using
tree-based properties. Function name is 'evolutionary_rate' or 'evo_rate'

1.2.2

- Added function to get the subtree of the last common ancestor among
a set of taxa

1.2.0

- Added command line interfaces for all functions so that each command
can more easily be executed. For example, 'phykit aln_len -h' can now be
called using 'pk_aln_len -h'

1.1.2

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

1.1.0

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

1.0.3

- Added rooting procedure before calculating RF to handle comparing
unrooted and rooted trees

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.

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

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

0.0.9

- PhyKIT now handles error stemming from piping output