Overview: new algorithms, methods and utilities

PhyML is a software package that uses modern statistical approaches to build phylogenetic trees from the analysis of alignments of nucleotide or amino acid sequences. The main tool in this package builds phylogenies under the maximum likelihood criterion. It implements a large number of substitution models coupled to efficient options to search the space of phylogenetic tree topologies.

The version that you can try inline on this page is PhyML 3.3. You can get and install it by downloading the code from https://github.com/stephaneguindon/phyml/.

Installation

Get the latest version !
You would find all PhyML releases here : https://github.com/stephaneguindon/phyml/releases

After unpacking the archive, go into the phyml/ folder and type the following command:

sh ./autogen.sh;

If you are using a Mac computer or running a Unix-like operating system, you will need to install the packages autoconf automake and pkg-config. On a Mac, the following command should set you up (provided Homebrew is installed on your Mac…): brew install pkg-config autoconf automake;

Next, to install any program that is part of the PhyML package, type the following commands:

./configure --enable-phyml;
make;

To compile a Windows executable, install MinGW and run:

./configure --enable-win --enable-phyml;
make;

To install the MPI version of PhyML, type the following commands:

autoreconf -i;
./configure --enable-phyml-mpi;
make;