Substitution model dependent on clades. For each clade a substitution model is specified. For nodes that do not fit in a clade a default substitution model is used.
defaultModel, tree, cladeModel, clades, taxa, frequencies
| type: beast.base.evolution.substitutionmodel.SubstitutionModel |
| Default substitution model, that is, the model that applies when none of the other do |
| Required input |
| type: beast.base.evolution.tree.Tree |
| tree for which to produce substitution models |
| Required input |
| type: beast.base.evolution.substitutionmodel.SubstitutionModel*** |
| substitution model for each of the clades specified |
| Optional input |
| type: beast.base.evolution.alignment.TaxonSet*** |
| set of taxa forming a clade and any branch in the clade will get a clade substitution model |
| Optional input |
| type: beast.base.evolution.alignment.Alignment |
| set taxa to choose from |
| Required input |
| type: beast.base.evolution.substitutionmodel.Frequencies |
| substitution model equilibrium state frequencies |
| Optional input |