Here are the comments I received for the Ne-estimator question recently posted here. Many thanks to everyone who responded: ----------------------- The choice of program will strongly depend on whether your are co-estimating population size with other population genetic forces, how much you favour speed over precision etc. For single (isolated) populations many/all program will do a good job. Try these based on the coalescent and use a microsatellite mutation model (stepwise or an approximation to that) Migrate (Beerli): http://popgen.scs.fsu.edu takes into account gene flow among populations, parallelized over loci, uses stepwise and Brownian motion approximation Lamarc (Kuhner et al): http://evolution.gs.washington.edu/lamarc takes into account gene flow, recombination exponential growth, uses stepwise and Brownian motion approximation IM and IMa (Hey and Nielsen): http://lifesci.rutgers.edu/~heylab/HeylabSoftware.htm takes into account gene flow among 2 populations and allow for divergence from an ancestral population Roychudhury and Stephens: http://www.genetics.org/cgi/content/full/176/2/1363 estimates single scaled population size fast Beast (Drumond, Rambaut et al): http://beast.bio.ed.ac.uk/Main_Page estimates a single population with variable models for changes of population size over time Batwing: Wilson and Balding: http://www.mas.ncl.ac.uk/~nijw/ I have certainly missed many other programs and ignore the programs based on frequencies, Peter Beerli ----------------------- We have created a program to infer Ne from a single sample of microsatellite data. You can use the program at http://genomics.jun.alaska.edu/ David Tallmon ----------------------- IM and Migrate are good for Ne estimation, so are Mark Beaumont's programs. For program descriptions and links, see my Microsatellites page on http://softlinks.amnh.org Best, Sergios-Orestis Kolokotronis ----------------------- a nice program implementing 6 different Ne techniques is NeEstimator from the Ovenden Lab (available at http://www2.dpi.qld.gov.au/fishweb/13887.html ). Input format is a genepop format and it is quite easy to use. good luck Gregory Maes ----------------------- Best, Martin Mag. Martin Koch Department of Zoology University of Graz Universitätsplatz 2 8010 Graz Austria martin.koch@uni-graz.at phone: +43 316 380 8756 http://www.kfunigraz.ac.at/zoowww/personal/mkoch/koch.htm martin.koch@uni-graz.at