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AstrobioMike
/
GToTree
A user-friendly workflow for phylogenomics
GNU General Public License v3.0
192
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25
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Save downloaded genomes from NCBI
#95
jmtsuji
opened
4 weeks ago
2
Alignment file empty
#94
aelbehery
closed
1 month ago
5
Using gtt-data-locations set with singularity image
#93
nandan75
closed
2 months ago
3
gtt-hmms only reports info for pre-built hmms
#92
AstrobioMike
opened
2 months ago
0
adding taxonomy info not working when run in nucleotide mode
#91
AstrobioMike
closed
1 month ago
2
remove doubling of genus if requesting genus and species
#90
AstrobioMike
opened
2 months ago
0
file name spacing issue with gtt-get-accessions-from-gtdb
#89
AstrobioMike
opened
2 months ago
0
GTDB metadata URL change
#88
ThinkPad254
closed
3 months ago
2
getting a `CERTIFICATE_VERIFY_FAILED` when running `gtt-get-accessions-from-GTDB`
#87
ctb
closed
3 months ago
3
can't seem to find a place to store startup environmental variables
#86
nandan75
opened
4 months ago
6
Error with pfam_counting.py
#85
SandersonHaley
closed
4 months ago
3
pfamA.txt.gz missing from ftp?
#84
SandersonHaley
closed
4 months ago
2
Unable to continue after **NOTICE**
#83
ReneKat
closed
7 months ago
2
GTDB Download - Latest path file extensions changed
#82
gdangelo8
closed
6 months ago
5
Bad metadata URLs in gtt-check-or-setup-GTDB-files
#81
jmtsuji
closed
8 months ago
2
fix logic to return True when the date_retrieved file is empty
#80
hyphaltip
closed
10 months ago
1
wiki fix
#79
hyphaltip
closed
11 months ago
1
Connection issue?
#78
corkdagga
closed
11 months ago
15
Create a nucleotide alignment
#77
Sidduppal
closed
1 year ago
6
Alignment file missing
#76
morgansobol
closed
11 months ago
4
Add check for input genome file not having line return after last input genome (renamed by Mike)
#75
Calvin2077
opened
1 year ago
4
current version fails downloads with openssl / curl errors
#74
spleonard1
closed
1 year ago
6
provide protein sequence or hmm for searching in lieu of pfam
#73
spleonard1
closed
1 year ago
2
HTTP error with downloading and parsing archaeal and bacteria metadata tables from GTDB
#72
oduwoleiyanu
closed
1 year ago
7
Issue with using GTDB
#71
Ahmed-Shibl
closed
1 year ago
4
Construct the tree of Virus and searching the metabolic genes
#70
Tsingsjeen
closed
1 year ago
3
Table with location(s) of SCG markers
#69
gkatahon
closed
1 year ago
1
Bioconda recipe
#68
vinisalazar
closed
1 year ago
9
Test run error
#67
asuria25
closed
1 year ago
4
Problem downloading the Actinobacteria.hmm
#66
oduwoleiyanu
closed
1 year ago
3
need to update pfam searching now that it's hosted by interpro
#65
AstrobioMike
closed
1 year ago
2
Same as closed issue #29 - runs successfully but .tre file is empty when using -m flag
#64
kellikmullane
closed
1 year ago
4
Feature request: subset-GTDB-accession options at family/genus/species level
#63
gabriellerocap
closed
1 year ago
6
Problem using -D to add GTDB lineage info to genome labels
#62
gabriellerocap
closed
1 year ago
3
Is this tool suitable for rodents?
#61
kuangzhuoran
closed
1 year ago
2
restarting GToTree
#60
nicholascdove
closed
1 year ago
5
Muscle Thread Usage
#59
raufs
closed
2 years ago
2
Trimal shows errors when prodigal amino acid file is provided to GToTree
#58
brymerr921
closed
2 years ago
1
GTDB database update today
#57
Tsingsjeen
closed
2 years ago
2
Alphaproteobacteria (0 targets)
#56
ebervilla
closed
1 year ago
5
duplicate entries
#55
Tsingsjeen
closed
2 years ago
2
Cleaning Trees with TreeShrink
#54
joshuakirsch
closed
2 years ago
1
Xs in alignment, Error codes in "Finished aligning and formatting gene-set steps"
#53
gkatahon
closed
2 years ago
2
Is this gzip step necessary?
#52
joshuakirsch
closed
2 years ago
3
Alignment for 'Bacteria' SCG set is only 169 AA long
#51
emily-ebel
closed
2 years ago
9
hmmsearch issue with large target sequence
#50
gavinmdouglas
closed
2 years ago
5
Adding KO scan capabilities and many other improvements
#49
AstrobioMike
closed
2 years ago
0
new muscle support
#48
jianshu93
closed
2 years ago
5
Alignment not loaded error during Aligning, trimming, and inserting gap-sequences step
#47
MiAiM
closed
2 years ago
4
Failed to make temporary directory
#46
susheelbhanu
closed
1 year ago
10
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