Description

Produces a Newick format phylogeny from a multiple sequence alignment using the maxium likelihood 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

*.{treefile}
included in
pathogensurveillance
authors
Github user avantonder Github user aunderwo
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

iqtree
GPL v2-or-later

Efficient phylogenomic software by maximum likelihood.

http://www.iqtree.org http://www.iqtree.org/doc https://github.com/iqtree/iqtree2 10.1093/molbev/msaa015