Software

The Structured Ancestral Recombination Graph (SARG)

This package contains the coalescent simulation software I have used in a number of papers. It differs from other standard packages (e.g. Hudson's) in that it allows things like balancing selection. The basic model used is described in Nordborg and Innan (2003). The most important difference is that it generates the ancestral recombination graph itself: mutations are added separately. This is useful for studying the behavior of the graph, and it also allows for flexibility in generating samples while conditioning on the aspects of the graph. It is not the best approach for rapidly generating large numbers of samples under standard assumptions, however.

The package is written in C++ and utilizes Mathematica as a front-end. A Mathematica package for drawing trees and calculating standard statistics is included. Please be forewarned that the C++ code, although reasonably cleanly written, is largely un-documented, and can be difficult to compile with older compilers (it uses a lot of advanced template instantiation). The code can easily be uncoupled from Mathematica, if you know C++.