Divergence, Diversity,
Informative Sites and
Phylogenetic Analyses

Phylogeny/Divergence/Diversity by PhyML 3.3.20220408

Data Input
Upload sequence alignment file Phylip Fasta Example
Sequence data type
Job seed   Fixed Randomized
Substitution Model
Substitution model
Equilibrium frequencies
Transition/transversion ratio   Fixed Estimated
Proportion of invariable sites   Fixed Estimated
Number of substitution rate categories
Gamma distribution parameter   Fixed Estimated
Tree Searching
Optimise tree
Branch Support
Compute aLRT   Yes No
Perform bootstrap   Yes No
Divergence/Diversity measurements   *Defining groups and selecting sequences for calculating divergence are on the next page, after you click "Submit & Email Results".
Calculate divergence/diversity based on
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When using PhyML please cite the following paper: Guindon S., Dufayard J.F., Lefort V., Anisimova M., Hordijk W., Gascuel O., New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0. Systematic Biology, 59(3):307-21, 2010.