Dear EvolDir members, I've got several request for a summary of answers to my query regarding software for scoring AFLP. I received positive comments on GeneMarker, which is very encouraging, but I haven't heard much about most other programs apart from Genographer - that seemed to have mixed references. So please if you or your colleagues have experience with alternative AFLP scoring software, I'd still be interested in hearing from you! Best wishes, Sarka jahodova@natur.cuni.cz RESPONSES I RECEIVED UP TO DATE (original post at the end): Just to let you know that I own a copy of GeneMarker, and am very happy with it. I use it for data from an ABI 3730, and prefer it to GeneMapper, which I have also used, but refused to buy because of the cost. I've heard that there's a lite-version, free, of GeneMapper, and once I find the lead I'll send it to you. If you're familiar with using this kind of software then GeneMarker is great. The manual assumes you've already used something like GeneMapper. I like the flexibility in the software, and also the ability to create panels that don't require you to go through so many peaks each time, once you've identified the informative markers in a population, species, etc. I tried to use Genographer and STRand, and got fed up, realizing that for high-throughput work, they would really get on my nerves after a while. Bob Marra ***** We have tried GeneMarker and found it an excellent program - it is very powerful and user-friendly. We routinely use GeneMapper and although GeneMarker is more user-friendly, these two programs give broad comparable results. Both GeneMarker and GeneMapper are fully automated (cf. Genographer). Also, I don't think Genographer supports the LIZ size standard. SoftGenetics allow you to download either a limited-function version, or a full-functional 30-day trial version of GeneMarker ( http://www.softgenetics.com/downloads.html ). We haven't had much experience with other programs, but you may find Table 1 in the attached paper helpful - it profiles most of the AFLP scoring software currently available. (Meudt, H.M. & Clarke, A.C. (2007) Almost Forgotten or Latest Practice? AFLP applications, analyses and advances. Trends in Plant Science, 12. p106-117.) Andrew Clarke & Heidi Meudt ****** I have experience working with both GeneMarker and Genotyper for genotyping AFLP traces, and can report that GeneMarker is a much better program. In fact, I genotyped three primer combinations of about 300 samples with Genotyper and with GeneMarker. Genotyper is simply not set up for this kind of work, and was generally cumbersome and difficult to work with, although I've been pleased with it before for genotyping microsatellite traces. GeneMarker is set up specifically for AFLPs (but works well to genotype microsatellites too), and the technical support is reasonably good. It allows you to correct for peak saturation and pullup between dyes, among other things, and does automatic genotyping of AFLP peaks in a way that makes a lot of sense to me, but is flexible as well. It does some things that are a little annoying, but may be corrected in the most recent update. For example, it re-sorts the marker table sometimes when you insert an allele (so you have to sort the table so the samples are arranged in order again, A1, A2, A3, etc.). It is also not possible to edit the marker table until you export into different software, such as Word or Excel. Kevin ***** I've never used GeneMarker, but just a few things to mention. 1. Have you thought about using a 650 Rox ladder? When I did my AFLPs using a 3100 ABI I found that I had quite a few fragments as large as 450bp, so LIZ wasn't an adequate ladder for me. 2. If you're cost limited, why not try BinThere? http://hcgs.unh.edu/protocol/aflp/AFLPbinthere.html It's free, downloadable software that I've heard is pretty good at auto-binning (particularly attractive for a large data set). I ran my samples through Genotyper (to define the ladder) and then used Genographer - by far my favourite software for analyzing my AFLP data. What type of problems did you have with it? Rachel Genographer definitely will have size standard issues unless you analyze the data with GeneScan first - I'm not exactly sure what it does, but I think it might calibrate the ladder.... when you've analyzed the files with GeneScan the file itself is changed and then they should work fine in Genographer. I liked this software because it created a virtual gel - made looking at many samples at the same time possible (plus another group of neat features related to assessing peak height and exact size). If you decide to give it another try I'm happy to help you figure stuff out. I've forwarded your email to a colleague who introduced me to BinThere - I'm not sure how much he knows about it, but I do know that he was pretty happy with the help he received from the program developer...I've asked him to get in touch if he thinks he has helpful info to tell you... Rachel Vallender ****** We did use BinThere in 2002 for our AFLP study. It is still available for download here (http://hcgs.unh.edu/protocol/aflp/AFLPbinthere.html) It is a mac-only application. It's advantages are that it is automatic (hence no subjectivity) and fast. However, I think it makes many more errors than a careful by-eye binning procedure would. Subsequent to this study, we used Genographer. John P. Sullivan ****** Thank you for getting back to us. We looked into BinThere a few months back, and I seem to recall that it's no longer supported (the woman who created it is now a yoga instructor - no longer in science). Apparently it can be modified by any user to do new things, but I don't think it is compatible with modern fluorescent data (e.g., with a LIZ size standard). Cheers, Andrew & Heidi ****** ORIGINAL POSTING: Dear EvolDir members, We are planning to purchase GeneMarker (from SoftGenetics) to score our AFLP profiles generated on ABI 3100 capillary system (using LIZ size standard). I would like to hear your experience with this software and possibly also comparison with other similar software. I would be particularly keen to hear about GelQuest, STRand and Peak Scanner (as I have not used them before) or comparison with Genotyper (the one I am most familiar with). We have a large sample size (about 2000 samples and 9 primer combinations in 3 multiplexes) and are thus looking for a high throughput software with automatic processing, that would allow manual editing and would be versatile and easy to use. We are limited by cost, so not considering GeneMapper etc. I had previously also tried Genographer, but encountered some problems. Many thanks, Sarka -- Sarka Jahodova Department of Ecology Charles University Vinicna 7 CZ-128 44 Prague 2 Czech Republic ------------------ Tel. +420 221951809 E-mail: jahodova@natur.cuni.cz And Department of Invasion Ecology Institute of Botany Academy of Sciences of the Czech Republic CZ-252 43 Pruhonice Czech Republic ------------------- http://www.ibot.cas.cz/invasions jahodova@natur.cuni.cz