(I resend this message, as it does not seem to have been delivered the first time). Thanks to all who replied to my question about metapopulation genetics simulation software. The original question was: Can anybody suggest a software package for individual based metapopulation genetics simulation of diploid organisms under different population sizes, migration rates, migration models and extinction-recolonisation rates. The program should be able to output genetic parameters at every generation (or every ten-hundred generations). Easypop does not seem to have an option of incorporating extinction-recolonisations. The software packages suggested: SimuPop - to be programmed in Phython Rmetasim and Kernelpop - to be programmed in R Mendelsaccountant Nemo quantiNemo simcoal2 Ecogenetics - being developed The packages simcoal2 and quantiNemo appear to be relatively easy to use, although in simcoal2 (and simcoal) making the input file work can sometimes be difficult. I am currently experimenting with these two packages and you are welcome to contact me a little later, if you want to learn more about my experience. Regards, Asta *** Original replies From: Paul Craze [mailto:P.Craze@sussex.ac.uk] It depends exactly what you want and how quickly you need it. Over the next few months I'm going to be developing a program to do something similar to what you describe and I could always try incorporating the kind of things you need (as well as making it more user-friendly than programs I write just for my own use!). Anyway, it might be an option to think about if it turns out there is no off-the-shelf software that'll do what you need. ** there are not much simulation softwares enabling many evolutionary scenarios. Easypop is indeed a good one to start, two others are also useful (also never used them myself), namely Mendelsaccountant (http://mendelsaccountant.info/) and SimuPop (http://simupop.sourceforge.net/index.php?option=3Dcom_content&task=3Dview&id=14&Itemid=49&PHPSESSID=079f19c6d701054b662d66903326dcdb). Please forward me the responses you get, as I am interested to hear if any new programs exist or is in development. ** try rmetasim and kernalpop. See Allan's website (http://linum.cofc.edu/software.html). it does exactly what you are attempting ** I have developed software to do just this. There are two R packages on CRAN that implement 1) patchy sites with a migration matrix and 2) continuous space (potentially broken into patches). The former is called rmetasim the latter, kernelpop. Both are lots more flexible than easypop, but with flexibility comes complexity. You need to use R to use the packages, though I'd argue that learning R would be useful for lots of other things as well. ** Regarding individual based modeling software- give Nemo a look. It isn't quite as ready out of the box as you are looking for, but it can do everything you are look for it to do. ** quantiNEMO does exactly what you are looking for. We just (yesterday) have it accepted by Bioinformatics. Extinction - recolonization can be simulated in two ways, either by setting an extinction rate for the populations, but in this case the extinction is random, or you specify the extinction explicitly by setting temporarily the carrying capacity of a patch to zero. The program itself and an extensive manual can be found at http://www2.unil.ch/popgen/softwares/quantinemo/. ** Nemo is an individual-based, genetically and spatially explicit simulation software. You can use it to model any kind of metapopulation structure with extinction/colonization, explicit sex- specific dispersal matrices (or island/stepping stone/lattice models), extended choice of mating systems, etc. It implements neutral genetic markers and deleterious mutations, for examples of two genetic traits that are already implemented. You can save the results at any pace you want during the simulation. The stats you can save for the neutral markers are F-stats (Gst & Theta), coancestries, heterozygosities, allelic diversity, Nei's D, etc. Plus you can save the population genotypes in FSTAT file format for subsequent analysis. Nemo is a command line tool. It's free and distributed under the GNU General Public License. You can download the source, documetatoin, and binaries (executable files) for Mac and Windows at the following URL: http://sourceforge.net/project/showfiles.php?group_id=3D161751 ** SimuPOP is able to do it, but you have to program it in Python. The mailing list is helpful (The author, Bo Peng, tends to help a lot) and the documentation is quite nice. But you will have to program the model. ** I suggest you take a look at the R package called Rmetasim, written by Allan Strand (Strand 2002 MolEcolNotes 2 (3):373-376). It is really flexible. It helps if you are already familiar with R. ** try simcoal or simcoal2 * We are developing a user-friendly simulation package, called ECOGENETICS with an individual-based module that allows defining all kinds of species and landscape geometries: Landscape: Patch topology and connectivity Patch size Patch extinction rate Effect of inter-patch environment on dispersal Life-cycle: Birth Survival Reproduction Dispersal Aging Death Density-dependent behaviour Sex-dependent behaviour Gene-dependent behaviour Random behaviour Clonal, hermaphrodite (with selfing) or sexuate reproduction Generation overlap Genetics: Neutral genetics Up to 8 loci, with up to 256 alleles Autosomal, X, Y chromosomes and mitochondrial KAM and stepwise mutation regime Input: Graphic interface for the patch topology. Inter-patch environment compatible with GIS Idrisi and Biomapper format User-friendly interface for the definition of the life-cycle Batch mode for sensitivity analyses Batch mode for Approximate Bayesian Computation (ABC) Output: Text files (for easy work with R) Compatible with F-Stat and Pop-Gen Various graphics for the preliminary simulations Wright's statistics Pedigree You can download a poster presenting EcoGenetics (with a few screenshots): Small format (4.76 Mb): http://www2.unil.ch/biomapper/ecogenetics/Hirzel-Ecogenetics-2008.pdf Big format (7 Mb): http://www2.unil.ch/biomapper/ecogenetics/Hirzel-Ecogenetics-2008-Poster.pdf Please contact me (Alexandre.Hirzel@unil.ch) if you are interested by a collaboration. ** Asta Audzijonyte Monterey Bay Aquarium Research Institute audzi@mbari.org audzi@mbari.org