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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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Bipartitions missing when transferring node label
#369
mesti90
closed
1 year ago
3
Difference between "N" (ambiguous code ) and "-" (gap)
#368
snakano0527
closed
1 year ago
1
Update alignment generation methods
#367
nickjcroucher
closed
1 year ago
1
Running error of "core dumped"
#366
aslangabriel99
closed
12 months ago
1
Error after 5 iterations
#365
mudymudy
closed
1 year ago
2
Numba issues
#364
leabednarczuk
closed
1 year ago
3
Add script for quantifying recombination per gene
#363
nickjcroucher
closed
1 year ago
0
Iteration1: Failed while building the tree with snippy-clean.aln
#362
rajneeshdadwal
closed
1 year ago
10
A problem for intermediate files
#361
userivy
closed
12 months ago
4
Error: Bipartitions missing when harmonising roots between trees
#360
eam12
closed
12 months ago
7
Ignore excluding sequence which has missing data
#359
snackens
closed
1 year ago
1
Gubbins using the WGS alignment created using contigs
#358
snackens
closed
1 year ago
1
Multiple outgroups may inflate execution time
#357
stitam
closed
1 year ago
2
Seems like gubbins failing to run on ~2500 whole genome alignemnt
#356
UzmaBasit
closed
1 year ago
11
generate recombination prediction regions only
#355
DorothyTamYiLing
closed
1 year ago
2
Very different trees using Gubbins and IQ-Tree
#354
alanxelena
closed
1 year ago
8
Illegal instruction (core dumped) Unable to fit model to data
#353
DorothyTamYiLing
closed
1 year ago
2
generate_ska_alignment.py problem (version 2)
#352
mstagliamonte
closed
2 years ago
7
abnormal bases in recombinations
#351
QianGuoPKU
closed
1 year ago
1
Merge in capacity to generate time-calibrated trees
#350
nickjcroucher
closed
2 years ago
0
KeyError: Not all labels matched to taxa
#349
pgcudahy
closed
2 years ago
2
mask_gubbins_aln.py issue
#348
Dangoh
closed
2 years ago
6
generate_ska_alignment.py problem
#347
aslangabriel
closed
12 months ago
2
I use run_gubbins.py -P to test and get an error, but I don't know how to solve it, please help
#346
xianglongwei
closed
2 years ago
6
Reference base in VCF file
#345
ramadatta
closed
12 months ago
0
Run has already reached the number of specified iterations
#344
nicolettacommins
closed
12 months ago
3
Description of extensive-search mode?
#343
nicolettacommins
closed
12 months ago
1
Issue 325
#342
nickjcroucher
closed
2 years ago
0
Add validation of datasets being combined
#341
nickjcroucher
closed
2 years ago
1
Can gubbins be used as a replacement for hyphy GARD or 3seq?
#340
phiweger
closed
2 years ago
4
Typo in manual: .final_tree.tree
#339
ezherman
closed
2 years ago
1
v3.2.1
#338
nickjcroucher
closed
2 years ago
0
Running raxML without -AVX2 options
#337
slmiles
closed
12 months ago
8
Gubbins not showing full data when adding a reference. help asap please
#336
ragheedk
closed
2 years ago
6
problem of installing gubbins from the repository
#335
liuqian666
closed
2 years ago
4
Fix tests
#334
jdaeth274
closed
2 years ago
0
Question: r/m calculation with CI95%!
#333
Tonny-zhou
closed
2 years ago
3
Error in running
#332
sekhwal
closed
2 years ago
3
Jar memory fixes
#331
jdaeth274
closed
2 years ago
0
Coordinates in the output file "Recombination predictions in GFF format"
#330
valery-shap
closed
2 years ago
2
Add tests for reconstruction accuracy
#329
nickjcroucher
closed
2 years ago
0
Improvements to reconstruction algorithm
#328
nickjcroucher
closed
2 years ago
1
Josh editing branch
#327
jdaeth274
closed
2 years ago
0
Unable to build a hybrid tree in v3.0.0
#326
UzmaBasit
closed
2 years ago
1
Bipartitions missing when transferring node label transfer
#325
annarerra
closed
2 years ago
31
gubbins 3.1.4 bioconda
#324
annarerra
closed
2 years ago
4
Improve testing
#323
nickjcroucher
closed
2 years ago
1
Switch from nosetest -> pytest
#322
nileshpatra
closed
2 years ago
0
mask_gubbins_aln.py
#321
xuechunxu
closed
12 months ago
3
Gubbinsv3.1.4 hash symbol # to dash symbol _
#320
drxilu
closed
12 months ago
2
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