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

fasta

*.fasta:file

Filtered variant alignment in fasta format

*.{fasta}

gff

*.gff:file

Recombination predictions in gff format

*.{gff}

vcf

*.vcf:file

SNP distribution

*.{vcf}

stats

*.csv:file

Per branch statistics

*.{csv}

phylip

*.phylip:file

Filtered variant alignment in phylip format

*.{phylip}

embl_predicted

*.recombination_predictions.embl:file

Recombination predictions in embl format

*.{recombination_predictions.embl}

embl_branch

*.branch_base_reconstruction.embl:file

Branch base reconstruction

*.{branch_base_reconstruction.embl}

tree

*.final_tree.tre:file

Recombination removed RAxML phylogenetic tree

*.{final_tree.tre}

tree_labelled

*.node_labelled.final_tree.tre:file

Recombination removed RAxML phylogenetic tree (nodes labelled)

*.{node_labelled.final_tree.tre}

versions

versions.yml:file

File containing software versions

versions.yml

Tools

gubbins

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