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biobakery
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phylophlan
Precise phylogenetic analysis of microbial isolates and genomes from metagenomes
https://huttenhower.sph.harvard.edu/phylophlan
MIT License
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Running partial workflow
#121
AroneyS
opened
8 months ago
1
Trouble running example 2 - Tree of Life
#120
sierra-smith
opened
10 months ago
0
The generated phylogenetic tree is missing MAGs at the leaf nodes.
#119
ylei14
opened
10 months ago
0
broken link on wiki
#118
jorondo1
opened
10 months ago
0
Reducing number of RAxML threads to 20, as it appears to underperform with more threads
#117
ylei14
opened
10 months ago
2
What is the difference between "phylophlan" database and "SGB.XXX"?
#116
augfranco93
opened
1 year ago
2
[e] gene_markers_identification crashed
#115
kaw97
opened
1 year ago
1
Can not download the phylophlan database
#114
jiaojiaoguan
closed
1 year ago
0
RAxML can't parse alignments for which there are sequences made entirely of undetermined characters
#113
RyanCook94
opened
1 year ago
1
phylophlan_metagenomic.py - offline usage
#112
fahad3li
closed
1 year ago
1
UnboundLocalError: cannot access local variable 'uniprotkb2uniref90' where it is not associated with a value
#111
chennyhui
opened
1 year ago
0
Mapping with Diamond v2 seems slow
#110
ganiatgithub
opened
1 year ago
1
maybee update taxa2core_cpa* to recent uniprot release
#109
EricDeveaud
opened
1 year ago
0
Prefiltering added to phylophlan_metagenomic.py
#108
kmladenovic
closed
8 months ago
0
Restart from checkpoint function available
#107
ganiatgithub
closed
1 year ago
1
How can I use my own database?
#106
EdderDaniel
closed
1 year ago
2
[e] mapping file (--maas) not specified
#105
IRSINGH27
closed
1 year ago
2
[e] No alignments found to concatenate
#104
jwkkang
opened
1 year ago
1
Phylophlan Error
#103
afedynak
opened
1 year ago
3
FastTreeMP returned non-zero exit status 1.
#102
gabridinosauro
opened
1 year ago
8
mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')
#101
PabloArrow
opened
1 year ago
1
Seems unable to find input faa files
#100
ganiatgithub
opened
1 year ago
1
Error: returned non-zero exit status 2
#99
GriffyGe
opened
2 years ago
1
UnboundLocalError: local variable 'uniprotkb2uniref90' referenced before assignment
#98
llk578496
closed
2 years ago
8
Bootstrap error obtained. zsh: killed
#97
pavlo888
opened
2 years ago
1
AttributeError: module 'collections' has no attribute 'MutableMapping'
#96
Guan06
closed
2 years ago
2
set.py long description file name variation
#95
erinpnewcomer
opened
2 years ago
1
[Enhancement] Future plans for fungi
#94
llk578496
closed
2 years ago
2
uniprot database differing number of markers
#93
pavlo888
opened
2 years ago
4
Error while running S aureus example
#92
rajneeshdadwal
opened
2 years ago
1
RAxML bad base
#91
nicholascdove
closed
2 years ago
6
where is the log file
#90
pavlo888
opened
2 years ago
3
Add option to generate a nucl database from the Uniprot core proteins
#89
alexhbnr
opened
2 years ago
5
Error running Phylophlan
#88
rybioinf
opened
2 years ago
3
fix a param position in Exception call
#87
Hocnonsense
closed
2 years ago
0
Does Phylophlan support genome multiple alignment of samples as multiple contigs?
#86
ne1al
closed
1 year ago
3
Feature proposal: `tqdm` progressbar during execution of `phylophlan`
#85
valentynbez
opened
2 years ago
0
The download of reference genomes
#84
lipumpkin
opened
2 years ago
2
Problem running phylophlan
#83
itiago
opened
2 years ago
1
Error when running for Enterococcus faecium
#82
llk578496
closed
2 years ago
2
Mutation Rate Table output
#81
LisaCarraro
opened
2 years ago
2
Strains resolution
#80
LisaCarraro
opened
2 years ago
2
Diamond error
#79
LisaCarraro
closed
2 years ago
5
no inputs found, please check your params and inputs file extensions error
#78
nishu92
closed
2 years ago
8
[error] Command: raxmlHPC-PTHREADS-SSE3' returned non-zero exit status 255.
#77
Jimmyeric94
closed
2 years ago
5
[e] substitution matrix "pfasum60" not found in "phylophlan_substitution_matrices/"
#76
linss123
opened
2 years ago
5
Need help for understanding how phylophlan works
#75
RunJiaJi
closed
2 years ago
2
Can't seem to execute Phylophlan successfully!!
#74
redekarnr
closed
2 years ago
8
[BUG] `phylophlan_configs` folder does not exists
#73
Mxrcon
opened
2 years ago
18
number of genomes to download in phylophlan_get_reference
#72
fancyge
opened
2 years ago
2
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