Hi all, Many thanks to all who replied back to my query on microsatellite allele binning; here goes the combined feedback, hope this helps AVIK RAY 1. Mirjamvandevliet@hotmail.com MSatAllele Alberto F. 2009 MsatAllele_1.0: an R package to visualize the binning of microsatellite alleles /Journal of Heredity./ 100(3):394--397 I used it now for severeal years. Easy to use and you get a clear picture of most possible allele size and if alleles have unexpected sizes (differenent sizes not consisiten with the motif size). 2. olepais@googlemail.com There were a few methods published these past few years: http://tinyurl.com/3aj9mac I was quite happy using FlexiBin, an Excell macro from Amos et al. 2007 or MsatAllele, a R package from Alberto 2009. 3. s.schliehe-diecks1@stud.uni-goettingen.de I'm analyzing the microsattelites for my samples with genemapper from Applied Biosystems (I also run my samples on a sequenzer of Applied Biosystems). There you create allel ranges, before the program reads the allel size and you create them by using your samples as calibration. The programm detects where the the peks are and asigns those ranges to allel names (or numbers,letters). This way, I always got integer allel sizes. I don't know whether this helped. Cheers, Susanne 4. jsmf77@gmail.com I just found the Flexibin application. It is an excel sheet (so no software at all) for allele binding. You can download it from this web page. http://www.zoo.cam.ac.uk/zoostaff/meg/amos.htm They have also a PDF tutorial on how to use it.Go to the right panel, click on 'computer programs' . It is the first in the list. 5. reevesp@lamar.colostate.edu AMOS, W., HOFFMAN, J. I., FRODSHAM, A., ZHANG, L., BEST, S. and HILL, A. V. S. (2007), Automated binning of microsatellite alleles: problems and solutions. Molecular Ecology Notes, 7: 10-14. http://onlinelibrary.wiley.com/doi/10.1111/j.1471-8286.2006.01560.x/full 6. Sewall.Young@dfw.wa.gov I work for the Washington State Department of Fish and Wildlife in the Molecular Genetics Laboratory. We have worked with microsatellites, mostly on salmonids, for about 13 years. We have always run our samples on Applied Biosystems instruments (377, 3100, 3730) and used AB's software to call genotypes. We struggled for several years to resolve the binning problem. Finally I constructed an Excel spreadsheet to do it, and I am willing to share it with you if you would like. Conceptually, it identifies allele clusters by looking for gaps in the distribution of electrophoretic mobilities. We can enter a minimum gap size and it will adjust the allele clusters to satisfy the gap requirement that we specify. We import data by pasting-in columns from Genemapper output files. The mechanics are accomplished through formulas entered in cells rather than by running a macro. I would not describe the spreadsheet as elegant, but it allowed us to enforce standard binning in our lab, where data compatibility is important. Let me know if you would like to take a look at it and I will send you a copy and instructions for using it. -- Visiting Fellow (Post Doc) NCBS-TIFR GKVK Campus Bellary Road Bangalore-65 India 080-23666340 avik.ray.kol@gmail.com