Phylogenetic estimation using (Maximum) Likelihood

Versions 3.2.0, 3.3.20170530, 3.3.20180621
License GPLv2
Links biotools: phyml, doi: 10.1093/sysbio/syq010

PhyML is a software that estimates maximum likelihood phylogenies from alignments of nucleotide or amino acid sequences. The main strength of PhyML lies in the large number of substitution models coupled to various options to search the space of phylogenetic tree topologies, going from very fast and efficient methods to slower but generally more accurate approaches. PhyML was designed to process moderate to large data sets. In theory, alignments with up to 4,000 sequences 2,000,000 character-long can be processed. PhyML can process data sets made of multiple genes and fit sophisticated substitution models with heterogeneous components across partition elements.


With an activated Bioconda channel (see 2. Set up channels), install with:

conda install phyml

and update with:

conda update phyml


A Docker container is available at