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