Our new simulator has been published in MBE:
SGWE simulates genome-wide sequence evolution under several substitution models that may change along the genome and the phylogeny, following complex multispecies coalescent histories that can include recombination, demographics, longitudinal sampling, population subdivision/species history, and migration. A new feature is that the heterogeneity of the whole evolutionary process can be parameterized according to statistical prior distributions specified by the user.
SGWE is freely available from http://code.google.com/p/sgwe-project/
