| implemented by the following |
| bmodeltest.evolution.sitemodel.BEASTModelTest |
Defines mutation rate and gamma distributed rates across sites (optional) and proportion of the sites invariant (also optional).
Site model that jumps between with and without gamma sites, as well as with and without invariant sites
Bouckaert RR, Drummond AJ. bModelTest: Bayesian phylogenetic site model averaging and model comparison. BMC evolutionary biology. 2017 Dec;17(1):42.
doi:https://doi.org/10.1186/s12862-017-0890-6
hasGammaRates, hasInvariantSites, mutationRate, gammaCategoryCount, shape, proportionInvariant, substModel
| type: beast.base.inference.parameter.IntegerParameter |
| flag indicating whether gamma rate heterogeneity should be used (if 1) or not (if 0) |
| Required input |
| type: beast.base.inference.parameter.IntegerParameter |
| flag indicating whether invariant sites should be used (if 1) or not (if 0) |
| Required input |
| type: beast.base.inference.parameter.RealParameter |
| mutation rate (defaults to 1.0) |
| Optional input |
| type: java.lang.Integer |
| gamma category count (default=zero for no gamma) |
| Optional input. Default: 0 |
| type: beast.base.inference.parameter.RealParameter |
| shape parameter of gamma distribution. Ignored if gammaCategoryCount 1 or less |
| Optional input |
| type: beast.base.inference.parameter.RealParameter |
| proportion of sites that is invariant: should be between 0 (default) and 1 |
| Optional input |
| type: beast.base.evolution.substitutionmodel.SubstitutionModel |
| substitution model along branches in the beast.tree |
| Required input |