ATGC: PhyML

PhyML 3.0: new algorithms, methods and utilities

Please cite:
"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.

Get the latest PhyML releases from GitHub.

PhyML online execution

Input Data
Sequence alignment (PHYLIP format)	Drop alignment file here or	file DNA	example (AA file) (DNA file) amino-Acids

Substitution Model

User defined
Substitution model
Equilibrium frequencies
Transition / transversion ratio		fixed	estimated
Proportion of invariable sites		fixed	estimated
Rate across sites model
Number of substitution rate classes
Gamma shape parameter		fixed	estimated

Automatic model selection by SMS
Selection criterion		AIC (Akaike Information Criterion)	BIC (Bayesian Information Criterion)
If you use SMS, please cite: "SMS: Smart Model Selection in PhyML." Vincent Lefort, Jean-Emmanuel Longueville, Olivier Gascuel. Molecular Biology and Evolution, 34(9):2422-2424, 2017.

Optimization options
Starting tree(s)		file	BioNJ
Constraint tree		yes	no
Optimize tree topology?		yes	no
Optimize edge lengths?		yes	no
Add random starting trees Using random starting trees makes the tree search more thorough, increasing the likelihood to find a better tree	[# of starting trees ]	yes	no

Branch Supports
Fast likelihood-based methods		yes	no
Standard bootstrap analysis This is the "classical" (i.e., non-parametric) bootstrap analysis	[# of repeats ]	yes	no
Transfer bootstrap analysis This is the "new" bootstrap analysis as described in Lemoine et al. (Nature, 556 (7702), 452-456, 2018)	[# of repeats ]	yes	no

Extra options
Keep duplicate sequences during analysis By default, duplicate sequences are removed at the start of the tree building and then re-inserted at the end. Use 'yes' only if you encouter issues with the default settings		yes	no
Print site likelihood		yes	no
Infer ancestral sequences Generate an extra output file containing ancestral sequences		yes	no
Name of your analysis You may want to add a tag/name to your analysis. This is helpful in case you are analyzing the same data sets under different options (e.g., distinct models)

About you...
Academic Private company
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Help PhyML	Make a donation ! Our servers are running many PhyML analyses every day. In fact, we are currently performing more than 300,000 CPU hours of computation with PhyML on our plateform every year! Please donate using this link https://fondation-cnrs.org/en/donate/ select "Software support PhyML". Donations to PhyML via CNRS Fondation will be used to upgrade our computer servers and hire engineers that will help us maintain and optimize the code of PhyML.