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 is available on GitHub.

PhyML online execution

Input Data
Sequence alignment (PHYLIP format)

Drop alignment file here



Substitution Model

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...
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