PhyML

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.

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;

PhyML online execution

Input data
Drag and drop a file or click to browse.
No file selected
Upload an aligned PHYLIP, FASTA, or CLUSTAL file. FASTA/CLUSTAL are converted to canonical sequential PHYLIP without changing sequence content.
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 PhyML PhyML online Benchmarks Datasets Forum & FAQ Papers & contacts

Other tools

DExTER

DExTER

Overview DExTER (Domain Exploration To Explain gene Regulation) is a bioinformatics tool designed to automatically identify genomic regions whose nucleotide composition correlates with gene expression levels. Unlike traditional approaches focusing on short transcription factor binding sites (6-12 bp), DExTER detects Long Regulatory Elements (LREs) that can span tens to hundreds of nucleotides. This makes it…

Gene expression Gene regulation Sequence analysis Expression correlation analysis Regression analysis Sequence analysis Sequence motif discovery Gene expression matrix Nucleotide code Sequence motif (nucleic acid) CSV FASTA TSV
See more
WAVES

WAVES

Warning : This application is no longer maintained and out of date. If you’re interested in, just have a look to MYST Summary WAVES is a web application dedicated to bioinformatic tool integration. It provides an efficient way to implement a service for any bioinformatic software. Such services are automatically made available in three ways:…

See more
CompPhy

CompPhy

CompPhy: a web-based collaborative platform for comparing phylogenies CompPhy is a web platform dedicated to the collaborative handling of phylogenetic trees. Users can freely manage collections of trees and communicate on a common project. By collaborative, we mean that several users connected to the same project can manipulation at the same time trees from shared…

Data visualisation Phylogenomics Phylogeny Phylogenetic analysis Phylogenetic sub/super tree construction Phylogenetic tree editing Gene tree newick Nexus format
See more