name: gubbins 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. licence: ['GPL-2.0-only'] keywords: - recombination - alignment tools: - gubbins: description: Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins. homepage: https://sanger-pathogens.github.io/gubbins/ documentation: https://sanger-pathogens.github.io/gubbins/ input: - alignment: type: file description: fasta alignment file pattern: "*.{fasta,fas,fa,aln}" output: - versions: type: file description: File containing software versions pattern: "versions.yml" - fasta: type: file description: Filtered variant alignment in fasta format pattern: "*.{fasta}" - embl_predicted: type: file description: Recombination predictions in embl format pattern: "*.{recombination_predictions.embl}" - gff: type: file description: Recombination predictions in gff format pattern: "*.{gff}" - embl_branch: type: file description: Branch base reconstruction pattern: "*.{branch_base_reconstruction.embl}" - vcf: type: file description: SNP distribution pattern: "*.{vcf}" - stats: type: file description: Per branch statistics pattern: "*.{csv}" - phylip: type: file description: Filtered variant alignment in phylip format pattern: "*.{phylip}" - tree: type: file description: Recombination removed RAxML phylogenetic tree pattern: "*.{final_tree.tre}" - tree_labelled: type: file description: Recombination removed RAxML phylogenetic tree (nodes labelled) pattern: "*.{node_labelled.final_tree.tre}" authors: - "@avantonder"