Dear All, recently, I posted a request "looking for simulation too with serial sampling". I had many responses, thank you all for getting back to me. However, most of you who wrote back to me, were also looking for such a tool! Basically, it seems that two possibilities exist to do the job: i.e. - forward in time OR backward in time with serial sampling (like Serial Simcoal) - has a mutation model suitable for microsatellites (SMM or GSMM) - includes recombination - able to simulate complex demographies, including admixture 1. quantiNEMO http://www2.unil.ch/popgen/softwares/quantinemo/ Thanks to Samuel Neuenschwander, author of quantiNEMO, who wrote back to me. quantiNEMO was originally developed to simulate quantitative traits, however, it allows also to simulate genetic data, including microsatellites. Loci are placed on a genetic map with any chromosomes. It is individual-based, forward in time, and allows to obtain samples from any generations. A very attractive feature is that parameters can change with time, thus allowing for sampling from any user defined generations. quantiNEMO allows to simulate highly complex demographic histories including selection. I found it very easy to learn to use. The only drawback is speed... but we can forgive for the slowness given all the features! 2. simuPOP A very general and flexible simulation environment, written in Python. Very attractive, however, its use requires quite a bit of coding in Python. The SimuPOP community, however, might be able to help (see very positive response from Bo Peng below). If anyone would try and finds it faster than quantiNEMO I would be interested to hear from you! "If you cannot find a program that fits your need, you can use simuPOP, a general-purpose individual-based population genetics simulation environment, to write your simulation, provided that you or someone in your group can program in Python. Please refer to the simuPOP website (simupop.sourceforge.net) for more information and feel free to discuss your simulation in the simuPOP mailing list. We might even be able to help you implement your simulation if your project is interesting enough." Hope this helps many... All the best Kati Katalin Csilléry, post-doc TIMC-IMAG, équipe TIMB, Université Joseph Fourier, F 38706 Tel.: + 33 456 52 00 65 Katalin.Csillery@imag.fr