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{:bash}

:file

fasta alignment file

*.{fasta,fas,fa,aln}

Output

name:type
description
pattern

fasta{:bash}

*.fasta{:bash}

:file

Filtered variant alignment in fasta format

*.{fasta}

gff{:bash}

*.gff{:bash}

:file

Recombination predictions in gff format

*.{gff}

vcf{:bash}

*.vcf{:bash}

:file

SNP distribution

*.{vcf}

stats{:bash}

*.csv{:bash}

:file

Per branch statistics

*.{csv}

phylip{:bash}

*.phylip{:bash}

:file

Filtered variant alignment in phylip format

*.{phylip}

embl_predicted{:bash}

*.recombination_predictions.embl{:bash}

:file

Recombination predictions in embl format

*.{recombination_predictions.embl}

embl_branch{:bash}

*.branch_base_reconstruction.embl{:bash}

:file

Branch base reconstruction

*.{branch_base_reconstruction.embl}

tree{:bash}

*.final_tree.tre{:bash}

:file

Recombination removed RAxML phylogenetic tree

*.{final_tree.tre}

tree_labelled{:bash}

*.node_labelled.final_tree.tre{:bash}

:file

Recombination removed RAxML phylogenetic tree (nodes labelled)

*.{node_labelled.final_tree.tre}

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

gubbins

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

sanger-pathogens.github.io/gubbins
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