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"