Package pal.eval

Class DemographicLikelihoodValue

java.lang.Object
pal.eval.LikelihoodValue
pal.eval.DemographicLikelihoodValue

public class DemographicLikelihoodValue extends LikelihoodValue
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. Must be used in conjunction with DemographicClockTree!
Version:
$Id: DemographicLikelihoodValue.java,v 1.2 2001/07/13 14:39:13 korbinian Exp $
Author:
Alexei Drummond
  • Constructor Details

    • DemographicLikelihoodValue

      public DemographicLikelihoodValue(SitePattern sp)
      Parameter taking a site pattern.
  • Method Details

    • compute

      public double compute()
      compute log-likelihood for current branch lengths and model return negative log-likelihood
      Overrides:
      compute in class LikelihoodValue