Package pal.coalescent
package pal.coalescent
Classes to model population genetic processes using the coalescent.
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ClassDescriptionExceptions to do with coalescent models et cetera.A series of coalescent intervals representing the time order information contained in a (serial) clock-constrained tree.Simulates a set of coalescent intervals given a demographic model.interface defining a parameterized tree that includes demographic information.This class models coalescent intervals for a constant population (parameter: N0=present-day population size).This class models a population that grows exponentially from an initial population size alpha N0 at time y to a size N0 at time x until the present-day.This class models a population that grows exponentially from an inital population size alpha N0 to a present-day size N0.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).This abstract class contains methods that are of general use for modelling coalescent intervals given a demographic model.interface defining a parameterized tree that includes demographic information.This class models a population that grows exponentially from an inital population size alpha N0 to a present-day size N0.This class models an exponentially growing (or shrinking) population (Parameters: N0=present-day population size; r=growth rate).A series of coalescent intervals representing the time order information contained in a (serial) clock-constrained tree.A simple wrapper class for containing the results which may either be a number of trees, or a number of trees and alignments (in parallel arrays)Simulates a set of coalescent intervals given a demographic model.Skyline plot derived from a strictly bifurcating tree or a coalescent interval.