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
(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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