nickjcroucher gubbins issues

nickjcroucher / 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

159 stars 49 forks source link

issues

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How to restart a gubbins run using the --resume flag

#413 mattbird567 opened 3 weeks ago
1
Making a core SNP tree to go along with final.tre

#412 djbradshaw2 opened 1 month ago
3
REF and Reference do not match, is this expected?

#411 djbradshaw2 opened 1 month ago
2
raxmlHPC-AVX2 error

#410 douco-ai closed 4 weeks ago
4
Buffer overflow during model fitting

#409 Koen-vdl opened 1 month ago
6
ci: bump github actions versions

#408 afuetterer closed 1 month ago
3
Does Gubbins can be used for Mycobacterium tuberculosis?

#407 TaoCheng98 closed 2 months ago
5
Restart from iteration 4 stopping when entering main loop for Iteration 5

#406 djbradshaw2 opened 2 months ago
5
Uninstalling gubbins 3.3.5

#405 ajkarloss closed 2 months ago
1
Update branch with optimised C code

#404 nickjcroucher closed 2 months ago
0
Latest Gubbins installs Gubbins 2.3.4

#403 ajkarloss closed 2 months ago
1
Pyjar causing core dump

#402 DOH-JDJ0303 closed 3 months ago
7
Can Gubbins be used on eukaryotic genomes?

#401 Adamtaranto closed 3 months ago
1
Multithreading not working on v3.3

#400 Alejandro-PI closed 3 months ago
1
Unable to install gubbin

#399 dzc0104 closed 2 months ago
6
Conda Gubbins 3.3.4 : Not able to install

#398 ajkarloss closed 2 months ago
11
Update to 3.4.3

#397 nickjcroucher closed 2 months ago
1
RuntimeError: cannot cache function 'seq_to_int'

#396 hkaspersen closed 3 months ago
5
Conda Gubbins 3.3.3 : Not able to install

#395 ajkarloss closed 3 months ago
3
File names with spaces cause error

#394 johnlees closed 3 months ago
2
Gubbins input file error

#393 marianajeeb closed 3 months ago
1
New ska version and masking

#392 pgcudahy closed 3 months ago
5
conda env for latest Gubbins?

#391 ajkarloss closed 5 months ago
2
Enable seed specification

#389 nickjcroucher closed 7 months ago
0
Possibility to fix the seed - for testing purpose of reproducibility ? (enhancement)

#388 evezeyl closed 7 months ago
2
Update legend in plot_gubbins.R

#387 drxilu opened 8 months ago
0
how long does joint ancestral reconstruction with pyjar take?

#386 lagphase closed 7 months ago
1
mask_gubbins_aln.py not removing recombinant regions

#385 erinpnewcomer closed 7 months ago
9
Add plotting and fix OSX installation bug

#384 nickjcroucher closed 9 months ago
0
Upgrade to using ska2

#383 nickjcroucher closed 9 months 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 10 months ago
5
alignment in final tree

#381 tbazilegith closed 11 months ago
1
alignment to use in final tree

#380 tbazilegith closed 11 months ago
2
IQtree executable name for IQtree 2.x is iqtree2

#379 tillea closed 11 months ago
6
'Palindrome middle base not W/S: 78' in generate_ska_alignment.py

#378 jvfe closed 12 months ago
1
identifying the donor of recombination events

#377 evolbeginner closed 12 months ago
1
Tree only shows part of the isolates

#376 tbazilegith closed 7 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 7 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
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 7 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