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TheBrownLab
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PhyloFisher
PhyloFisher is a software package written in Python3 that can be used for the creation, analysis, and visualization of phylogenomic datasets that consist of eukaryotic protein sequences.
MIT License
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heterotachy.py error
#124
thesamuanels
opened
1 week ago
0
added lock
#123
DavidZihala
closed
2 months ago
0
Fix the bug in issue#120 "NameError: name 'metadata' is not defined"
#121
shuiyujinlan
closed
4 months ago
0
metadata not defined in forest_local.py
#120
sipesk
closed
4 months ago
7
matrix_constructor.py stops at 55 %
#119
Edouard94
closed
1 month ago
16
Integrates nucl matrix contsructor
#118
robert-ervin-jones
closed
4 months ago
0
add leaf rename utility
#117
robert-ervin-jones
closed
4 months ago
0
heterotachy.py handling of taxon names
#116
atice
opened
8 months ago
2
Add .circleci/config.yml
#115
robert-ervin-jones
closed
8 months ago
0
fix typo matrix_constructor.smk
#114
giacomomutti
closed
8 months ago
0
Duplicate and non-trimmed genes in matrix_constructor.py output
#112
cha-namoth
closed
9 months ago
4
Paralogs added have the exact same name as ortholog
#111
matiasWanntorp
opened
9 months ago
4
Running PhyloFisher across multiple nodes
#110
matiasWanntorp
closed
9 months ago
2
Options for amino/nuc and to write fastest sites out
#109
aguang
opened
10 months ago
3
Including BUSCO's metazoa_odb10 dataset
#108
dongzhang0725
closed
10 months ago
2
fast_site_remover.py with nucleic acid sequences
#107
aguang
opened
11 months ago
3
forest.py creates an empty folder
#106
AlexGalvez
closed
11 months ago
2
sgt_constructor.py "Could not create conda environment from /opt/anaconda3/envs/fisher/bin/bmge.yaml"
#105
AlexGalvez
closed
11 months ago
6
updates raxml tree path
#104
robert-ervin-jones
closed
12 months ago
0
Updates raxml ng
#103
robert-ervin-jones
closed
1 year ago
0
No bootstrap values
#102
mjamy
closed
11 months ago
16
Nucleotide alignments
#101
snacktavish
closed
12 months ago
3
apply_to_db.py does not update metadata.tsv file
#100
Edouard94
closed
1 year ago
5
Errors running sgt_constructor.py: `Error in rule prequal`, `Error in rule length_filter_mafft`
#99
mjamy
closed
1 year ago
8
adds sht_include option to informant
#97
robert-ervin-jones
closed
1 year ago
0
updates matrix_constructor_stats.tsv and adds occupancy.tsv
#96
robert-ervin-jones
closed
1 year ago
0
updates logic behind sanity check
#94
robert-ervin-jones
closed
1 year ago
0
updates forest_local to reflect change to raxml-ng
#92
robert-ervin-jones
closed
1 year ago
0
forest_local.py creates empty output folder
#91
anoukwillemsen
closed
1 year ago
4
updates raxml command to only use one thread
#90
robert-ervin-jones
closed
1 year ago
0
RAxML within sgt_constructor uses all available resources
#89
anoukwillemsen
closed
1 year ago
2
Getting error when running apply_to_db.py
#88
thesamuanels
closed
1 year ago
8
Geeting error when trying to run the select_taxa.py script
#87
robert-ervin-jones
closed
1 year ago
7
84 forestpy produces an empty directory
#85
robert-ervin-jones
closed
1 year ago
0
forest.py produces an empty directory
#84
miferg
closed
1 year ago
8
Fix select taxa chimera bug
#83
robert-ervin-jones
closed
1 year ago
0
Non-reproducible baseline example
#82
cafernandezlo
closed
1 year ago
1
index out of range error with select_taxa.py --chimera
#81
cha-namoth
closed
1 year ago
5
updates raxml rule to use raxml-ng
#80
robert-ervin-jones
closed
1 year ago
0
changes raxml threads
#79
robert-ervin-jones
closed
1 year ago
0
add support for singularity
#77
zhan4429
closed
1 year ago
3
Nucl matrix utility
#76
robert-ervin-jones
closed
1 year ago
0
adds trimal gt param to matrix_constructor.py
#75
robert-ervin-jones
closed
1 year ago
0
bumps version to 1.2.6
#74
robert-ervin-jones
closed
1 year ago
0
adds path to matrix_constructor.smk to setup.py
#73
robert-ervin-jones
closed
1 year ago
0
matrix_constructor.smk not found
#72
cha-namoth
closed
1 year ago
3
changes sgt to homolog in informant
#71
robert-ervin-jones
closed
1 year ago
0
fixes aa_recoder
#70
robert-ervin-jones
closed
1 year ago
0
aa_encode.py or SR4_class_recoder.py
#69
robert-ervin-jones
closed
1 year ago
1
reworks backup strategy
#67
robert-ervin-jones
closed
1 year ago
0
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