name: iqtree
description: Produces a Newick format phylogeny from a multiple sequence alignment using the maxium likelihood algorithm. Capable of bacterial genome size alignments.
keywords:
  - phylogeny
  - newick
  - maximum likelihood
tools:
  - iqtree:
      description: Efficient phylogenomic software by maximum likelihood.
      homepage: http://www.iqtree.org
      documentation: http://www.iqtree.org/doc
      tool_dev_url: https://github.com/iqtree/iqtree2
      doi: doi.org/10.1093/molbev/msaa015
      licence: ['GPL v2-or-later']

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: "*.{treefile}"

authors:
  - "@avantonder"
  - "@aunderwo"