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

versions (file)

File containing software versions

versions.yml

phylogeny (file)

A phylogeny in Newick format

*.{tre}

stockholm_alignment (file)

An alignment in Stockholm format

*.{sth}
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Github user aunderwo
Github user avantonder
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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.

birc.au.dk/software/rapidnj https://github.com/somme89/rapidNJ 10.1007/978-3-540-87361-7_10