coalesce

Coalescent simulator. More...

Classes
class	Arg
	Ancestral recombination graph. More...
class	Change
	Pure virtual base class for parameter changes. More...
class	SingleParamChange
	Pure virtual base class for single parameter changes. More...
class	PopulationParamChange
	Single parameter changes applied to a single population. More...
class	Bottleneck
	Bottleneck event. More...
class	PopulationBottleneck
	Population-specific bottleneck event. More...
class	AllPopulationSizeChange
	Change of the size of all populations. More...
class	SinglePopulationSizeChange
	Change of a single population size. More...
class	GrowthRateChange
	Change of the growth rate of all populations. More...
class	PopulationGrowthRateChange
	Change of a single population's growth rate. More...
class	SelfingRateChange
	Change of the selfing rate. More...
class	PopulationFusion
	Fusion of two populations. More...
class	PopulationSplit
	Split of a population. More...
class	AllMigrationRateChange
	Change of the migration rate of all population pairs. More...
class	SingleMigrationRateChange
	Change of a single migration rate. More...
class	Controller
	Controls a coalescent simulation. More...
class	Current
	Represents the current set of populations. More...
class	Edge
	Edge of the ancestral recombination graph. More...
class	EdgePool
	Pool of Edge objects. More...
class	Mutation
	Very simple container of some information relative to a mutation. More...
class	Mutator
	Implements mutation models. More...
class	ParamSet
	Set of parameters. More...
class	Population
	Handles a single population. More...

Detailed Description

Coalescent simulator.

The set of classes implements a three-scale coalescent simulator with recombination, and a flexible mutation model. The main classes are Controller (the starting point for generating genealogies), ParamSet (that centralizes parameter specification), the Change hierarchy (that implements demographic change specifications), Arg (ancestral recombination graph; the result of generation a genealogy) and Mutator (that generates genotype data from an ARG).