name: rapidnj
description: Produces a Newick format phylogeny from a multiple sequence alignment using a Neighbour-Joining algorithm. Capable of bacterial genome size alignments.
keywords:
  - phylogeny
  - newick
  - neighbour-joining
tools:
  - rapidnj:
      description: RapidNJ is an algorithmic engineered implementation of canonical neighbour-joining. It uses an efficient search heuristic to speed-up the core computations of the neighbour-joining method that enables RapidNJ to outperform other state-of-the-art neighbour-joining implementations.
      homepage: https://birc.au.dk/software/rapidnj
      documentation: https://birc.au.dk/software/rapidnj
      tool_dev_url: https://github.com/somme89/rapidNJ
      doi: "doi:10.1007/978-3-540-87361-7_10"
      licence: ["GPL v2"]

input:
  - alignment:
      type: file
      description: A FASTA format multiple sequence alignment file
      pattern: "*.{fasta,fas,fa,mfa}"

output:
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - phylogeny:
      type: file
      description: A phylogeny in Newick format
      pattern: "*.{tre}"
  - stockholm_alignment:
      type: file
      description: An alignment in Stockholm format
      pattern: "*.{sth}"
authors:
  - "@aunderwo"
  - "@avantonder"