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matsengrp
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gctree
GCtree: phylogenetic inference of genotype-collapsed trees
https://matsengrp.github.io/gctree
GNU General Public License v3.0
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131 Fix rendering hang when parent directory of output file doesn't exist
#132
willdumm
opened
14 hours ago
0
tree rendering hangs when write directory doesn't exist.
#131
jgallowa07
opened
1 week ago
1
Add filtering by reversions to naive sequence, generalize ranking strategy
#130
willdumm
closed
2 weeks ago
4
Handle truncated dnapars `outfile`s correctly
#129
willdumm
closed
2 months ago
0
Fix single ranking criterion bug
#128
willdumm
closed
4 months ago
0
Qt platform plugin could be initialized
#127
NSchwanPhy
closed
4 months ago
2
Poisson context likelihood and better cli flexibility
#126
willdumm
closed
4 months ago
0
Fix ufunc attribute error from numpy.log
#125
willdumm
closed
5 months ago
0
Extreme Runtime
#124
lejecrs
opened
6 months ago
5
Phylip Installaion
#123
vivekruhela
closed
6 months ago
4
Dependency and warning fix and compatibility with Scipy 1.12
#122
willdumm
closed
7 months ago
1
update historydag version requirement
#121
jgallowa07
closed
7 months ago
1
Disagreement in node coloring for (some) identical sequences
#120
victor-ramos
closed
8 months ago
6
Tree visualization without the number text
#119
markutz556
closed
6 months ago
2
fix gap character ambiguity bug
#118
willdumm
closed
1 year ago
0
Tree inference taking very long time - advice needed
#117
fabio-t
closed
9 months ago
11
Rethink isotype inference
#116
willdumm
opened
1 year ago
0
Python 3.10, and macOS integration testing
#115
wsdewitt
closed
1 year ago
0
GitHub action runner OS not set
#114
wsdewitt
closed
1 year ago
0
Incorrect dnapars outfile parsing
#113
willdumm
closed
2 months ago
0
rename master to main
#112
willdumm
closed
1 year ago
0
swap master --> main
#111
psathyrella
closed
1 year ago
1
Remove `S5F` contents and mark experimental features
#110
willdumm
closed
1 year ago
0
Allow all ranking stats to be computed on individual `CollapsedTree`s
#109
willdumm
opened
1 year ago
1
to support amino acids sequences
#108
cjhong
opened
1 year ago
1
Add option to recover all top-ranked trees instead of sampling from topology classes
#107
willdumm
opened
1 year ago
0
gctree infer with --tree-stats argument does not write pickled tree outputs
#106
willdumm
opened
1 year ago
1
ValueError: Zero likelihood event
#105
chaoszhang
closed
2 months ago
7
interface with SAMM or bypass Galton branching
#104
Lan-h
opened
1 year ago
7
jumble parameter in `mkconfig`
#103
wsdewitt
closed
2 years ago
0
Colormap enhancements
#102
wsdewitt
closed
2 years ago
0
Jumble parameter for tree space search should be user configurable
#101
wsdewitt
opened
2 years ago
6
Make gctree deterministic when ranking is degenerate
#100
willdumm
opened
2 years ago
1
local branching metric harmonization
#99
wsdewitt
opened
2 years ago
0
Rename master branch to main
#98
matsen
closed
1 year ago
0
Add full inference test and remove mutation model ignore_ualabel call
#97
willdumm
closed
2 years ago
1
Local branching metrics fixes
#96
wsdewitt
closed
2 years ago
2
Errors installing PyQt5 dependency on ARM Mac using pip
#95
wsdewitt
opened
2 years ago
0
Fix numpy errors on gctree import
#94
willdumm
closed
2 years ago
0
CLI to calculate parsimony scores
#93
willdumm
opened
2 years ago
0
`import gctree` causes `FloatingPointError` in independent matplotlib/numpy calls
#92
wsdewitt
closed
2 years ago
2
71 ambiguous input data
#91
willdumm
closed
2 years ago
2
Ability to count reversions
#90
matsen
opened
2 years ago
1
Simplify abundance logic and remove tuple sequence names
#89
willdumm
closed
2 years ago
1
Avoid tuple root node name
#88
willdumm
closed
2 years ago
2
stringified tuple sequence name
#87
psathyrella
closed
2 years ago
0
Fix multiple tree nodes with same name
#86
willdumm
closed
2 years ago
3
Address Duncan's suggestions
#85
willdumm
closed
2 years ago
0
Various comments/suggestions
#84
psathyrella
closed
2 years ago
3
add isotype to mutation model simulation
#83
willdumm
opened
2 years ago
1
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