Directories

Files
file	Coalescent.hpp [code]
	A lazy header to include the headers needed to start writing simulations. Includes: <Sequence/Coalescent/SimTypes.hpp> <Sequence/Coalescent/Coalesce.hpp> <Sequence/Coalescent/Recombination.hpp> <Sequence/Coalescent/Mutation.hpp> <Sequence/Coalescent/Initialize.hpp> <Sequence/Coalescent/DemographicModels.hpp> <Sequence/Coalescent/FragmentsRescaling.hpp>

file	FragmentsRescaling.hpp [code]
	Helper functions for simulating partially linked fragments One often wants to simulate partially linked fragments under neutral models. An efficient way to do this is to simulate a contiguous fragment, but with the recombination rate varying along the region (to represent the variable genetic distances between fragments). This header file declares functions that make this task easier, particularly the operations of rescaling the positions of mutations/marginal trees from the genetic map back to the physical map.

file	SimTypes.hpp [code]
	declaration of types for coalescent simulation

file	TreeOperations.hpp [code]

Files