| PhyML |
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PhyML
Infer a maximum-likelihood phylogenetic tree from an alignment.
Default settings
| Parameter | Default value |
|---|---|
| Sequence type | DNA (nucleotides) |
| Model selection | User-defined |
| SMS criterion | BIC |
| Equilibrium frequencies | Default: observed nucleotides / model amino acids |
| Invariable sites estimation | Estimate |
| Proportion of invariable sites | 0.0 |
| Rate variation model | Gamma distribution + invariable |
| Number of rate categories | 4 |
| Gamma shape estimation | Estimate |
| Gamma shape parameter | 1.0 |
| DNA substitution model | HKY85 |
| Transition/transversion estimation | Estimate |
| Transition/transversion ratio | 4.0 |
| Protein substitution model | LG |
| Starting tree | BioNJ |
| Constraint tree | No constraint |
| Optimize tree topology | Yes |
| Optimize branch lengths | Yes |
| Add random starting trees | No |
| Number of random starting trees | 5 |
| aLRT support | SH-like aLRT |
| Standard bootstrap analysis | No |
| Number of bootstrap replicates | 100 |
| Transfer bootstrap analysis | No |
| Number of transfer bootstrap replicates | 100 |
| Keep duplicate sequences | No |
| Print site likelihood | No |
| Infer ancestral sequences | No |
Enter data and configure this analysis
See the documentation for input formats, result downloads and scientific references.
phylogeny.atgc-montpellier.fr is provided by the ATGC bioinformatics platform.
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