'Dear all, below a selection of the responses I got regarding the question of available open source/free microsatellite genotyping software. Thanks for all the great suggestions, this helps a lot. Peter >ABI just came out with a free software for scoring alleles (based on profiles from an ABI machine, of course). It's called Peak Scanner. Does some of the same things that you can do in Genotyper or Genescan - but better because it's free. I've been using Peak Scanner lately, it's very user friendly - quite simple really, in practice and scope, which may or may not be a limitation for some people. It seems to work great for me. Hope this helps.   >Strand from the University of Davis which is very stable software and quite user-friendly once you learn how it works. You can find it here: http://www.vgl.ucdavis.edu/informatics/strand.php There is a good user manual and FAQ. It can handle files from ABI sequencers both capillary and slap gels. There is no automatic binning procedure (allele size are just rounded) but you can export the exact allele size (in pb) and then binn your alleles using various available methods, for instance: FlexiBin (excel macro) : http://www.zoo.cam.ac.uk/zoostaff/amos/ Amos et al. 2006 Mol Ecol Notes MsatAllele (R package) : which specifically refered to STRand http://www.ccmar.ualg.pt/maree/software.php?soft=msatalle Alberto 2009 Journal of Heredity Allelogram : may also be usefull. Morin et al., 2009 Mol Ecol Ressources 9 (6)   >We have recently developed a PERL pipeline for dealing with microsatellite data called P2EMA. It is meant to easy the painful task of dealing with microsat data. P2EMA is a Perl/Tk graphical user interface (GUI) that facilitates several tasks when scoring microsatellites. It does so by implementing new subroutines in R and PERL and taking advantage of features provided by previously developed software such as PeakScanner, CREATE and AlleloBin. P2EMA allows running PeakScanner easily from the commandline, analysing markers from several multiplex groups simultaneously, manual bin definition through a new R script (Binator), direct bin definition through AlleloBin and file conversion through CREATE. Please, do not hesitate to send us any comments on your experience with P2EMA and recommendations as how it could be improved. You can get the P2EMA pipeline and post your comments at the P2EMA project webpage: http://sourceforge.net/projects/p2ema/ An application note has been submitted to Bioinformatics: F Palero, F González-Candelas and M Pascual (submitted) P2EMA (Perl Pipeline for Easy Microsatellite Analysis) - a user-friendly package. Bioinformatics.'   Peter Hoebe Crop & Soil Systems Scottish Agricultural College King's Buildings Edinburgh EH9 3JG +44 (0)131 535 4370   Peter Hoebe