Package pal.eval

Classes for evaluating evolutionary hypothesis (chi-square and likelihood criteria) and estimating model parameters.

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.
 

Package pal.eval Description

Classes for evaluating evolutionary hypothesis (chi-square and likelihood criteria) and estimating model parameters.