Uses of Interface
pal.tree.ParameterizedTree

Packages that use ParameterizedTree
pal.coalescent Classes to model population genetic processes using the coalescent. 
pal.eval Classes for evaluating evolutionary hypothesis (chi-square and likelihood criteria) and estimating model parameters. 
pal.tree Classes for providing the data structure of trees, for constructing and modifying trees, and for parameterizing trees (e.g., clock constraint). 
 

Uses of ParameterizedTree in pal.coalescent
 

Classes in pal.coalescent that implement ParameterizedTree
 class DemographicClockTree
          Provides parameter interface to a clock-like genealogy which is assumed to have some demographic pattern of theta (diversity) as well as branch parameters (the minimal node height differences at each internal node).
 

Uses of ParameterizedTree in pal.eval
 

Methods in pal.eval with parameters of type ParameterizedTree
 double[] ModelParameters.estimateFromTree(ParameterizedTree t)
          estimate (approximate) values for the model parameters from the data using a given (parameterized) tree
static double LikelihoodOptimiser.optimiseAlternate(ParameterizedTree tree, Alignment alignment, SubstitutionModel model, MultivariateMinimum minimiser, int fxFracDigits, int xFracDigits)
          Optimise parameters to acheive maximum likelihood using an alternating stategy.
static double LikelihoodOptimiser.optimiseAlternate(ParameterizedTree tree, Alignment alignment, SubstitutionModel model, MultivariateMinimum minimiser, int fxFracDigits, int xFracDigits, MinimiserMonitor monitor)
          Optimise parameters to acheive maximum likelihood using an alternating stategy.
static double LikelihoodOptimiser.optimiseCombined(ParameterizedTree tree, Alignment alignment, SubstitutionModel model, MultivariateMinimum minimiser, int fxFracDigits, int xFracDigits)
          Optimise parameters to acheive maximum likelihood using a combined stategy.
static double LikelihoodOptimiser.optimiseCombined(ParameterizedTree tree, Alignment alignment, SubstitutionModel model, MultivariateMinimum minimiser, int fxFracDigits, int xFracDigits, MinimiserMonitor monitor)
          Optimise parameters to acheive maximum likelihood using a combined stategy.
static double LikelihoodOptimiser.optimiseTree(ParameterizedTree tree, Alignment alignment, SubstitutionModel model, MultivariateMinimum minimiser, int fxFracDigits, int xFracDigits)
          Optimise tree branchlengths only to acheive maximum likelihood using a combined stategy.
static double LikelihoodOptimiser.optimiseTree(ParameterizedTree tree, Alignment alignment, SubstitutionModel model, MultivariateMinimum minimiser, int fxFracDigits, int xFracDigits, MinimiserMonitor monitor)
          Optimise tree branchlengths only to acheive maximum likelihood using a combined stategy.
 

Uses of ParameterizedTree in pal.tree
 

Classes in pal.tree that implement ParameterizedTree
 class ClockTree
          provides parameter interface to a clock tree (parameters are the minimal node height differences at each internal node)
 class LogParameterizedTree
          This class logarithmically transforms tree parameters.
 class MutationRateModelTree
          Provides parameter interface to any clock-like tree with serially sampled tips (parameters are the minimal node height differences at each internal node).
 class UnconstrainedTree
          provides parameter interface to an unconstrained tree (parameters are all available branch lengths)
 

Methods in pal.tree that return ParameterizedTree
 ParameterizedTree ParameterizedTree.Factory.generateNewTree(Tree base)
          Generate a new parameterized tree wrapped around base
 

Constructors in pal.tree with parameters of type ParameterizedTree
LogParameterizedTree(ParameterizedTree params)
          Takes a parameterized object and transforms the parameters logarithmically.