PhyML 3.0

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

Stéphane Guindon Jean-François Dufayard Vincent Lefort Maria Anisimova Wim Hordijk Olivier Gascuel

10.1093/sysbio/syq010

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.

Installation

To install PhyML, download the code from https://github.com/stephaneguindon/phyml/. 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;

PhyML 3.0 online execution

Input data
Drag and drop a file or click to browse.
No file selected
Upload a PHYLIP formatted alignment file.
Let MYST infer the alignment alphabet, or force nucleotide/amino-acid mode.
Substitution Model
Choose between automatic Smart Model Selection (SMS) or manual parameters.
Automatic model selection (SMS)
Criterion used by SMS to rank candidate models.
User defined model parameters
How equilibrium base or amino-acid frequencies are determined.
Choose whether to estimate the proportion of invariable sites.
Proportion of sites with zero substitution rate.
Specify how rate variation across sites is handled.
Number of discrete rate categories (for gamma models).
Choose whether to estimate the gamma shape parameter.
Shape parameter for the gamma rate distribution.
Substitution Model (DNA)
Substitution model applied to nucleotide sequences.
DNA transition parameters
Whether to estimate the transition/transversion ratio or use a fixed value.
Ratio of transition to transversion rates (DNA only).
Substitution Model (Protein)
Substitution model applied to amino-acid sequences.
Optimization options
Starting tree used to initiate the search.
User starting tree
Drag and drop a file or click to browse.
No file selected
Upload the custom starting tree in Newick format.
Optionally provide a tree to constrain the search space.
Constraint tree
Drag and drop a file or click to browse.
No file selected
Constraint tree in Newick format.
Random starting trees
Specify how many random starting trees should be generated.
Control whether tree topology is optimized.
Control whether branch lengths are optimized.
Add additional random starting trees to the search.
Branch supports
Fast branch support method.
Perform non-parametric bootstrap replicates.
Standard bootstrap settings
Specify the number of standard bootstrap replicates.
Extra options
Preserve duplicate sequences instead of collapsing them.
Output per-site likelihood values.
Infer ancestral sequences for internal nodes.
PhyML 3.0 PhyML 3.0 PhyML 3.0 online Benchmarks Datasets Forum & FAQ Papers & contacts Versions

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