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"