For general use, I would like to recommend Hudson's ms, which is
definitely the most popular one of all. This masterpiece is also very
efficient, qualified for most practical uses. MaCS seems also a
competent candidate, but maybe more publications are needed to justify
its practical performance.
I have used the following softwares or carefully read their
publications and documentations:
ms, by Hudson.
Type: standard coalescent-with-recombination; backward in time;
Features: allows for simulating various events such as variable
population size, recombination, gene conversion, migration and
Type: approximation to the standard coalescent (see below); backward in time; discrete time
Approximation: The following sentence indicate the difference
between GENOME and ms: "In the standard approach, each
coalescent event involves exactly two sequences that coalesce to a
common ancestor but, using our approach, multiple sequences can
coalesce to a common ancestor simutaneously". I am not sure
how this may affect the accuracy of simulation, but the comparison
between ms and GENOME seems to be satisfactory.
Features: variable population size, recombination and symmetric
migration. Claim to be fast.
Notes: My experience is GENOME is not as fast as MaCS, although
the performance is highly related to the heuristic parameters in
use. In addition, this software requires recombinations to happen
between segments which may affect the accuracy of very ancient