Description

Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions.

Input

Name (Type)
Description
Pattern

alignment (file)

fasta alignment file

*.{fasta,fas,fa,aln}

Output

Name (Type)
Description
Pattern

versions (file)

File containing software versions

versions.yml

fasta (file)

Filtered variant alignment in fasta format

*.{fasta}

embl_predicted (file)

Recombination predictions in embl format

*.{recombination_predictions.embl}

gff (file)

Recombination predictions in gff format

*.{gff}

embl_branch (file)

Branch base reconstruction

*.{branch_base_reconstruction.embl}

vcf (file)

SNP distribution

*.{vcf}

stats (file)

Per branch statistics

*.{csv}

phylip (file)

Filtered variant alignment in phylip format

*.{phylip}

tree (file)

Recombination removed RAxML phylogenetic tree

*.{final_tree.tre}

tree_labelled (file)

Recombination removed RAxML phylogenetic tree (nodes labelled)

*.{node_labelled.final_tree.tre}
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Tools

gubbins

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins.

sanger-pathogens.github.io/gubbins