-
Notifications
You must be signed in to change notification settings - Fork 8
/
change_log.txt
143 lines (109 loc) · 5.08 KB
/
change_log.txt
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
Major changes to PhyKIT are summarized here.
1.21.0
- The partition file outputted from the create_concat function has been updated
- Column information in the partition file is as follows:
- column 1: alignment name
- column 2: # of taxa present
- column 3: # of taxa missing
- column 4: fraction of occupancy
- column 5: names of missing taxa (; separated)
1.20.0
- Fixed bug for thread_dna function when using a ClipKIT log file. Input protein alignment must be the untrimmed alignment.
1.19.4
- Saturation function forces y-intercept to be zero when calculating slope
1.19.3
- Saturation function now uses uncorrected distances instead of pairwise identities
1.19.2
- Verbose pairwise identity reporting separates pairwise identities by tabs and not a dash
1.19.0
- Added function to test for site-wise compositional biases in an alignment. See function compositional_bias_per_site.
1.18.0
- Added function to estimate site-wise evolutionary rate in an alignment. See function evolutionary_rate_per_site.
1.15.0
- Added function to recode alignments based on 8 different recoding schemes (7 for amino acids;
1 for nucleotides). See function recode
1.14.0
- 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/).
1.12.6
-relative composition variability is now adapted for calculating compositional biases in
individual taxa. The new function in rcvt (relative composition variability, taxon).
1.12.4
- 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
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