| Package | Description |
|---|---|
| Likelihood |
Provides classes for calculating the likelihood of a tree given a model and
an alignment.
|
| Modifier and Type | Method and Description |
|---|---|
R |
Calculator.calculate(Parameters p)
Abstract method for actually calculating the likelihood
|
abstract R |
Calculator.combineSites(java.util.Map<Site,SiteLikelihood> sites,
Parameters p)
Combines the likelihood from each site into a alignment likelihood
|
StandardLikelihood |
StandardCalculator.combineSites(java.util.Map<Site,SiteLikelihood> sites,
Parameters p) |
Range |
ConfidenceInterval.getCI(Parameter param,
double conf)
Calculates the confidence interval for a single parameter
|
protected java.util.Map<Site,SiteLikelihood> |
Calculator.siteCalculate(Parameters p)
Calculates the likelihood for each site
|