PhyML Maximum Likelihood
The Building Phylogenetic Tree dialog for the PhyML Maximum Likelihood method provides the following view:
The following parameters are available:
Substitution model parameters - a selection of the Markov model of substitution:
- Substitution model - model of substitution.
- Equilibrium frequencies - equilibrium frequencies.
- Transition/transversion ratio - fix or estimate the transition/transversion ratio in the maximum likelihood framework.
- Proportion of invariable sites - the proportion of invariable sites, i.e., the expected frequency of sites that do not evolve, can be fixed or estimated.
- Number of substitution rate categories - the number of substitution rate categories.
- Gamma shape parameter - the shape of the gamma distribution determines the range of rate variation across sites.
Branch support parameters - the selection of the method used to measure branch support:
- Use fast likelihood method - use fast likelihood method.
- Perform bootstrap - the support of the data for each internal branch of the phylogeny can be estimated using non-parametric bootstrap.
Tree searching parameters - the selection of the tree topology searching algorithm:
- Make initial tree automatically - initial tree automatically.
- Type of tree improvement - type of tree improvement.
- Set number of random starting tree - the number of random starting trees.
- Optimize tree topology - the tree topology is optimized to maximize the likelihood.
- Optimize branch lengths - optimize branch lengths.
- Optimise substitution rate - substitution rate parameters are optimized.
Display tree in new window - displays tree in a new window.
Display tree with alignment editor - displays tree with an alignment editor.
Synchronize alignment with tree - synchronize alignment and tree.
Save tree to - file to save the built tree.
Press the Build button to run the analysis with the selected parameters and build a consensus tree.