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See:
Description
Interface Summary | |
LikelihoodCalculator | classes that calculate likelihoods should implement this interface. |
Class Summary | |
ChiSquareValue | computes chi-square value of a (parameterized) tree for its set of parameters (e.g., branch lengths) and a given distance matrix |
DemographicLikelihoodValue | Estimates the likelihood for a tree using a specified model of sequence evolution and a sequence alignment and a specific demographic model as a prior on coalescent intervals. |
DemographicValue | estimates demographic parameters by maximising the coalescent prior for a tree with given branch lengths. |
FastLikelihoodCalculator | Title: Fast Likelihood Calculator Description: A fast likelihood calculator Original code by Matthew Goode. |
LikelihoodValue | Computes the likelihood for a tree given a model of sequence evolution and a sequence alignment; also optimises tree parameters such as branch lengths by maximising the likelihood (for optimal performance special optimisation procedures are employed for UnconstrainedTree, ClockTree and DatedTipsClockTree; a general optimisation precedure is used for another ParameterizedTree). |
ModelParameters | estimates substitution model parameters from the data |
SimpleLikelihoodCalculator | Only to be used by one thread. |
Classes for evaluating evolutionary hypothesis (chi-square and likelihood criteria) and estimating model parameters.
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