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.

PhyML now includes Smart Model Selection. SMS can also be used on its own.

If you use SMS, please cite:
"SMS: Smart Model Selection in PhyML."
Vincent Lefort, Jean-Emmanuel Longueville, Olivier Gascuel.
Molecular Biology and Evolution, msx149, 2017.

PhyML online execution

Input Data
Sequences
(PHYLIP format)
File Example (AA file) (DNA file)
(from Phylogenetic Handbook)
Data Type DNA Amino-Acids

Substitution Model

Tree Searching
Starting tree(s) File BIONJ
Type of tree improvement
Number of random starting tree yes no

Branch Support
Fast likelihood-based method Use aLRT or aBayes to save computing time yes no
Perform bootstrap yes no

Name of your analysis
Your email
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