Class bpp::ClockTreeLikelihood: See GlobalClockTreeLikelihoodFunctionWrapper as a more general replacement.
Class bpp::DiscreteRatesAcrossSitesClockTreeLikelihood: See GlobalClockTreeLikelihoodFunctionWrapper as a more general replacement.
Member bpp::OptimizationTools::optimizeNumericalParametersWithGlobalClock (DiscreteRatesAcrossSitesClockTreeLikelihood *cl, const ParameterList &parameters, OptimizationListener *listener=0, unsigned int nstep=1, double tolerance=0.000001, unsigned int tlEvalMax=1000000, OutputStream *messageHandler=ApplicationTools::message, OutputStream *profiler=ApplicationTools::message, unsigned int verbose=1, const std::string &optMethodDeriv=OPTIMIZATION_GRADIENT): See optimizeNumericalParameters2 as a more general replacement.
Member bpp::OptimizationTools::optimizeNumericalParametersWithGlobalClock2 (DiscreteRatesAcrossSitesClockTreeLikelihood *cl, const ParameterList &parameters, OptimizationListener *listener=0, double tolerance=0.000001, unsigned int tlEvalMax=1000000, OutputStream *messageHandler=ApplicationTools::message, OutputStream *profiler=ApplicationTools::message, unsigned int verbose=1, const std::string &optMethodDeriv=OPTIMIZATION_GRADIENT): See optimizeNumericalParameters2 as a more general replacement.
Class bpp::RHomogeneousClockTreeLikelihood: See GlobalClockTreeLikelihoodFunctionWrapper as a more general replacement.
Member bpp::TreeTools::midpointRooting (Tree &tree): Use TreeTemplateTools::midRoot instead!