Phylogenetic inference for molecular evolution using PhyML

PhyML Plugin

PhyML estimates maximum likelihood phylogenies from alignments of nucleotide or amino acid sequences. PhyML offers a 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.

Quick Start

Install the plugin by downloading the gplugin file and dragging it in to Geneious Prime or use the plugin manager in Geneious Prime (under Tools - Plugins in the menu).

Once installed, run the plugin by selecting a multiple sequence alignment and clicking on Tree in the toolbar. PhyML is available as an option at the top of the Tree building options window.


2.2.4 (06 Mar 2019) – Download for Geneious 10.0

– Updated included PhyML to version 3.3.20180621

– Show PhyML version number in the options dialog

2.2.3 (27 Mar 2017) – Download for Geneious 6.0

– Fixed crash on Windows when running from a data directory containing certain non-Latin characters (e.g., Chinese)

– Fixed crash that would occur when running with a custom substitution model on Windows machines

2.1.0 (29 Jun 2012) – Download for Geneious 5.1

– Added custom substitution model option, can be used with ModelTest output

– Added optimization option (Topology/Length/Rate)


"New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0." Guindon S., Dufayard J.F., Lefort V., Anisimova M., Hordijk W., Gascuel O. Systematic Biology, 59(3):307-21, 2010.


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