gubbins

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snippy+ gubbins

3

I have questions when using snippy + gubbins: 1) When I use reference in snippy does it have to be reference from the same dataset or well annotated genome? 2)...

nbawe

Restart Gubbins after the execution was cancelled due to cluster time limit

1

Hi, Is there a way to restart and ask Gubbins to use already generated Raxml/intermediate files from the last executed step? Thanks,

alipirani88

The average values of r/m and rho/theta for the whole dataset

1

Hi, I am using Gubbins to detect recombination in a dataset of Vibrio genomes . Gubbins gave values of r/m and rho/theta for each branch in output file ".per_branch_statistics.csv". My...

hngyou

Output not just polymorphic sites:

10

Hiya, I'm wondering if it's possible to output the whole filtered alignment (including invariant sites). I want to run BEAST after Gubbins, which has issues with only using polymorphic sites....

EisenRa

How to eliminate false-positive

2

Hi, I ran Gubbins in 35 E. coli samples. I got around 14 samples with SNPs

Noornoor440

Using Gubbins on bactsnp resutls

1

I'm trying to understand how the gubbins software works based on results obtained with bactsnp. I wanted to test with a bacterial genome, CP025268.1 (knowing that I have to do...

roxmila

Why some isolates are removed by Gubbins

6

I have 1500 aligned sequences in fasta file, but 5 of them are removed after Gubbins , there are 1495 isolates in ***filtered_polymorphic_sites.fasta** and ***final_tree.tre** files, anyone know the reason,...

zhaoxvwahaha

RE: Maximum-Likelihood trees from Iqtree, raxml, fasttree etc The scale is not SNPs, it is substitutions per site. These are (subtly) different. ie. A->T->A is two subs but not a...

fengyuchengdu

Gubbins with masked input alignment

2

I'm trying to use Gubbins but want to mask certain regions in my analysis. For example, I want to exclude regions of the genome that tend to have issues with...

nicolettacommins

/src/alignment_file.c: line 302 code: return '\0'; regfree(&regex); }

maddin200