Software

The two programs below relate to the coalescent process in a continuous habitat. That is, populations that are not subdivided into discrete demes, but where geographic differentiation results from restricted gene flow. In each case, clicking the link will download a zipped file that contains all of the C source code, a Makefile, and a PDF document that describes how to use the program.

The programs have been developed on the command-line side of a Macintosh running OS X. Both programs have also been successfully built and run under Linux. Running the programs on your particular system may require some minor modifications to the Makefile.

MUTANT TRACKER

This is a program for simulating genealogies in a continuous habitat. Either a one-dimensional or two-dimensional habitat can be modeled. The program allows for certain heterogeneities, including variable population density, and range expansion or contraction. Output forms include raw genealogies, and data under an infinite-sites or stepwise (microsatellite) mutation model.

DIMPLE

DIMPLE (Demographic Inference by Maximum Partial Likelihood Estimation) performs parameter estimation in a one-dimensional, continuous habitat. The program implements two estimation procedures based on the solution for the distribution of pairwise coalescence times derived in Wilkins & Wakeley 2002. One method is based on regressing observed versus expected mean pairwise distances. The second is a composite likelihood solution based on the full distribution of pairwise coalescence times. Confidence intervals for both methods can be constructed using data simulated in the MUTANT TRACKER program.