These are the few replies we got to the following request: THANKS to everyone who responded. REQUEST: We would like to get an overview over user-friendly (ideally Mac & PC based) programs to 1) make linkage maps 2) calculate recombination rates 3) allow for different recombination rates of males and females 4) ideally be usable in diploids and polyploids We would like to apply the program to pedigree data using msats in parents and F1. Thanks for your suggestions in advance. Best, Matthias ***** Good morning These software are not the most user friendly, in that a hidden tab or space at the end of a file can crash it but they are windows based and can handle separate Male and Female maps. They were originally developed for salmonid fish which are ancestral polyploids. http://www.uoguelph.ca/~rdanzman/software/ Linkmfex ¡V mapping in male and female, allow to examine difference in recombination between the sexes and between individuals Probmax ¡V basic pedigree software, that will also allow you to examine if the marker panel you are using is sufficient to discern complete parentage Enjoy Peace D Darrin Reid, MSc, Biologist National Research Council of Canada Institute for Marine Biosciences Halifax, NS, B3H 3Z1 No doubt you will know about 'MapMaker', which is a nightmare. Someone recently introduced me to 'AntMap', which is interesting but doesn't do everything you request (sex differences). http://cse.naro.affrc.go.jp/iwatah/antmap/index.html Mike Ritchie School of Biology Dyers Brae House University of St Andrews St Andrews, Fife Scotland KY16 9TH Phone 0 (44 outside UK) 1334 463495 Fax 0 (44 outside UK) 1334 463366 Website: http://bio.st-andrews.ac.uk/staff/mgr.htm ***** The animal genomics research community has used Phil Green's Cri-Map program for the best part pf the last 15 years to compute linkage maps. The program will do everything that you ask (and in fact quite a bit more, since it will also construct IBD maps of the chromosomes of all individuals). It won't handle polyploids and it doesn't have a fancy GUI (it is command line driven), but it will handle very large pedigrees and large numbers of loci. We have just used the program to constuct a genetic map of over 12,000 SNPs scored in 10,000 individuals. You can get it here. http://linkage.rockefeller.edu/soft/crimap/ Jerry Taylor Wurdack Chair in Animal Genomics University of Missouri Matthias Stoeck