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nickjcroucher
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gubbins
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
http://nickjcroucher.github.io/gubbins/
GNU General Public License v2.0
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Problem to install on MacBook osx-amr64
#420
Fla1487
opened
1 day ago
0
Addition of multithreading
#419
nickjcroucher
closed
1 week ago
0
Analysing viral sequences
#418
a-qvecell
opened
1 month ago
0
Please add support for VeryFastTree
#417
marade
opened
1 month ago
0
docs: update README.md
#416
eltociear
closed
1 week ago
0
mask_gubbins_aln.py output contains sequences of unequal length
#415
shreyaramachandran
closed
1 month ago
1
Input File Error with Singularity/Apptainer
#414
whottel
opened
3 months ago
0
How to restart a gubbins run using the --resume flag
#413
mattbird567
opened
5 months ago
1
Making a core SNP tree to go along with final.tre
#412
djbradshaw2
closed
1 month ago
4
REF and Reference do not match, is this expected?
#411
djbradshaw2
opened
5 months ago
4
raxmlHPC-AVX2 error
#410
douco-ai
closed
5 months ago
4
Buffer overflow during model fitting
#409
Koen-vdl
opened
6 months ago
6
ci: bump github actions versions
#408
afuetterer
closed
5 months ago
3
Does Gubbins can be used for Mycobacterium tuberculosis?
#407
TaoCheng98
closed
6 months ago
5
Restart from iteration 4 stopping when entering main loop for Iteration 5
#406
djbradshaw2
opened
6 months ago
6
Uninstalling gubbins 3.3.5
#405
ajkarloss
closed
6 months ago
1
Update branch with optimised C code
#404
nickjcroucher
closed
7 months ago
0
Latest Gubbins installs Gubbins 2.3.4
#403
ajkarloss
closed
7 months ago
1
Pyjar causing core dump
#402
DOH-JDJ0303
closed
7 months ago
7
Can Gubbins be used on eukaryotic genomes?
#401
Adamtaranto
closed
7 months ago
1
Multithreading not working on v3.3
#400
Alejandro-PI
closed
7 months ago
1
Unable to install gubbin
#399
dzc0104
closed
6 months ago
6
Conda Gubbins 3.3.4 : Not able to install
#398
ajkarloss
closed
7 months ago
11
Update to 3.4.3
#397
nickjcroucher
closed
7 months ago
1
RuntimeError: cannot cache function 'seq_to_int'
#396
hkaspersen
closed
8 months ago
5
Conda Gubbins 3.3.3 : Not able to install
#395
ajkarloss
closed
8 months ago
3
File names with spaces cause error
#394
johnlees
closed
8 months ago
2
Gubbins input file error
#393
marianajeeb
closed
8 months ago
1
New ska version and masking
#392
pgcudahy
closed
8 months ago
5
conda env for latest Gubbins?
#391
ajkarloss
closed
9 months ago
2
Enable seed specification
#389
nickjcroucher
closed
12 months ago
0
Possibility to fix the seed - for testing purpose of reproducibility ? (enhancement)
#388
evezeyl
closed
12 months ago
2
Update legend in plot_gubbins.R
#387
drxilu
opened
1 year ago
0
how long does joint ancestral reconstruction with pyjar take?
#386
lagphase
closed
12 months ago
1
mask_gubbins_aln.py not removing recombinant regions
#385
erinpnewcomer
closed
12 months ago
9
Add plotting and fix OSX installation bug
#384
nickjcroucher
closed
1 year ago
0
Upgrade to using ska2
#383
nickjcroucher
closed
1 year ago
2
Why are some recombination events blue but at the same loci of red ones in the same pattern in 2 distant lineages?
#382
Isoris
closed
1 year ago
5
alignment in final tree
#381
tbazilegith
closed
1 year ago
1
alignment to use in final tree
#380
tbazilegith
closed
1 year ago
2
IQtree executable name for IQtree 2.x is iqtree2
#379
tillea
closed
1 year ago
6
'Palindrome middle base not W/S: 78' in generate_ska_alignment.py
#378
jvfe
closed
1 year ago
1
identifying the donor of recombination events
#377
evolbeginner
closed
1 year ago
1
Tree only shows part of the isolates
#376
tbazilegith
closed
12 months ago
5
Muliple sequence alignment as input
#375
tbazilegith
closed
1 year ago
1
Dockerfile for gubbins
#374
stitam
closed
1 year ago
1
what are the best parameters that can be use for identical sequences in Raxml?
#373
SachiiM
closed
1 year ago
1
RecursionError
#372
CSouque
closed
12 months ago
5
from numpy.core._multiarray_umath import ( KeyboardInterrupt
#371
qianxin-kxy
closed
1 year ago
1
generate_ska_alignment: error: unrecognized arguments: --input input.list
#370
qianxin-kxy
closed
1 year ago
10
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