Package pal.eval

Class 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 Detail

      • DemographicLikelihoodValue

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

      • compute

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