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.

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Input Data
Sequences
(PHYLIP format)		 File Example file
Data Type DNA Amino-Acids
Sequence file interleaved sequential
Number of data sets

Substitution Model
Substitution model LG model is new and tends to outperform JTT and WAG
Equilibrium frequencies
Transition / transversion ratio
(DNA models)		 fixed estimated
Proportion of invariable sites fixed estimated
Number of substitution rate categories
Gamma shape parameter fixed estimated

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