Description

Produces a Newick format phylogeny from a multiple sequence alignment using a Neighbour-Joining algorithm. Capable of bacterial genome size alignments.

Input

name:type
description
pattern

alignment:file

A FASTA format multiple sequence alignment file

*.{fasta,fas,fa,mfa}

Output

name:type
description
pattern

stockholm_alignment

*.sth:file

An alignment in Stockholm format

*.{sth}

phylogeny

*.tre:file

A phylogeny in Newick format

*.{tre}

versions

versions.yml:file

File containing software versions

versions.yml

Tools

rapidnj
GPL v2

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.