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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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Support for Python 3.10
#82
willdumm
closed
1 year ago
0
add potential Dockerfile + test.sh
#81
psathyrella
closed
2 years ago
8
Update installation docs
#80
willdumm
closed
2 years ago
0
Prerelease tidying
#79
wsdewitt
closed
2 years ago
0
Mutability chain split
#78
willdumm
closed
2 years ago
0
Update README.md
#77
wsdewitt
closed
2 years ago
0
Docs fixes
#76
wsdewitt
closed
2 years ago
0
Store isotype data in nodes
#75
willdumm
closed
2 years ago
0
Transplant patch
#74
wsdewitt
closed
2 years ago
0
Transplant docs
#73
wsdewitt
closed
2 years ago
0
Add ambiguous sequence test and error message
#72
willdumm
closed
2 years ago
0
accommodate ambiguous observed sequences
#71
willdumm
closed
2 years ago
7
Fix underflow errors on some machines by avoiding calling np.exp(-np.inf) in ll.
#70
willdumm
closed
2 years ago
3
LB metrics for CollapsedTree and sequence-based fitness for simulation
#69
wsdewitt
closed
2 years ago
0
Fit parameters on history DAG
#68
willdumm
closed
2 years ago
11
Consistent Numpy underflow error on some machines
#67
willdumm
closed
2 years ago
2
Any parallel or accelerated parameters?
#66
liyi522
closed
2 years ago
1
Add isotype utility
#65
willdumm
closed
2 years ago
0
restrict tuple-valued node names to bootstrap trees
#64
wsdewitt
closed
2 years ago
0
obey isotype switching order
#63
willdumm
closed
2 years ago
4
Use history DAG to find more maximum parsimony trees
#62
willdumm
closed
2 years ago
5
Disambiguate with mutability
#61
willdumm
closed
2 years ago
1
Uniqueness of IDs not necessary
#60
fabio-t
closed
1 year ago
1
Default help menu missing
#59
fabio-t
closed
2 years ago
1
Problem with Sequence IDs
#58
fabio-t
closed
2 years ago
10
Disambiguate trees using Sankoff Algorithm
#57
willdumm
closed
2 years ago
0
Phylip_parse.disambiguate sometimes chooses non-optimal tree
#56
willdumm
closed
2 years ago
0
a few tree rendering options
#55
wsdewitt
closed
3 years ago
0
Mlepatch
#54
wsdewitt
closed
3 years ago
0
find identical mamaras in the tree
#53
matsen
closed
2 years ago
10
update README (and potentially web link) with reference for full paper
#52
matsen
closed
3 years ago
1
Plot annotations
#51
wsdewitt
closed
3 years ago
0
Packagify
#50
wsdewitt
closed
3 years ago
0
Plot are not generated due to a problem with Qt
#49
Aurelien-Pelissier
closed
3 years ago
3
46 biopython upgrade
#48
wsdewitt
closed
3 years ago
0
colors in hex
#47
cstrlln
closed
3 years ago
2
Error: Biopython
#46
jonoave
closed
3 years ago
1
Error: scons: *** No SConstruct file found.
#45
jonoave
closed
3 years ago
3
Data inconsistency between simulation and inference
#44
NikaAb
closed
3 years ago
3
About the output file when using the --bootstrap option
#43
xvtyzn
closed
4 years ago
2
It is possible parallel processing in step python -u bin/gctree.py
#42
Chuang1118
closed
3 years ago
5
--idlabel not working?
#41
cstrlln
closed
4 years ago
2
use of color argument
#40
cstrlln
closed
4 years ago
3
Limit of abundance for each sequence
#39
NikaAb
closed
5 years ago
5
Fasta file with variable sequence length
#38
NikaAb
closed
5 years ago
2
Dockerfile, and a release
#37
matsen
closed
3 years ago
0
Installation or user idiocy problem
#36
vnminin
closed
6 years ago
6
Output the best tree as newick
#35
krdav
closed
6 years ago
0
cleaning repo for submission
#34
wsdewitt
closed
7 years ago
2
Multiple t
#33
krdav
closed
7 years ago
0
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