Hello everyone, I've collected all the responses I got to my AFLP/Microsat Scoring Software post..... Hope this helps others out there!
Krissa Skogen University of Connecticut Of the ones you listed, I only know GeneMarker. I am currently using it and not very impressed with that software; I definitely prefer GeneMapper. GeneMarker does not allow setting up a project and adding samples with time. Every time you add a sample, you need to start all over again with the analysis. Very cumbersome! I recently saw the software that comes with the Beckman Sequencers. I am not sure if it is available otherwise or it only works with the Beckman System, but it looked very user friendly and versatile to me. ---------------------------------------------------------------------------------------------------------- I have been using GeneMapper for microsats. I like it fine and the support is good but I have not been able to totally automate the allele calling. I am certainly no molecular wizard (just another ecologist wannabe), but in general I am happy with it. Best, Laura Meyerson ---------------------------------------------------------------------------------------------------------- I have used both Genemarker (for microsats and AFLP) and Genemapper (for microsats).The softgenetics inc software is far better (easier to get started, more intuitive, better structured) than the ABI software, and their customer support is far better too!...I tend to think ABI 'rest on their laurels' because they have such a large market share. I would go Softgenetics ---------------------------------------------------------------------------------------------------------- If your lab use ABI genotyper then GeneMapper is the best choice based on its function and convenience. But it is very expansive. GeneMarker is probably the best choice based on the compromising functionality and price. You can download a trial version and PDF manual from http://www.softgenetics.com/downloads.html. GeneMarker also supports different file formats of generated from the genotypers of other brands http://www.softgenetics.com/GeneMarker.html. Don't use GelCompar II (Applied Maths). It is user-unfriendly and very limited on number of lanes (about 150 lanes) in an analysis. This software transforms the curve signals of genotypes to a gel image file manually. You have to set molecular weight of internal standards for each experiment. ... many other drawbacks can make you crazy when you are scoring AFLP of large sample size. ---------------------------------------------------------------------------------------------------------- We use genemarker and are very happy with it. It has a couple of twitches which make it a little frustrating from time to time. For example after you have set up locus rules, you may want to add an allele that you didnt see before. Most times you can click the allele and add it to the locus, but other times (maybe 5% of the time) it wont let you.... but the cost makes it worthwhile! ---------------------------------------------------------------------------------------------------------- we've used GeneMapper, STRAND, and GeneMarker; I'd say for the average project GeneMarker is hands-down the easiest and extremely powerful, well worth its somewhat cheaper price (relative to GeneMapper). ---------------------------------------------------------------------------------------------------------- I was in similar situation earlier this year and decided to go for GeneMarker. And I'm quite happy with that. GeneMarker is capable of processing large number of samples, has automatic scoring option and allows manual editing. You can ask for a fully functional trial version (30days) and the technical support is very good. There are little things (with displaying, sorting, editing etc) that I would personally prefer to work differently, but they are planning some development on the software soon, so there might be some improvements soon. So can recommend :-) ---------------------------------------------------------------------------------------------------------- I'm facing the same problem and was going to get genographer, which does not do any automated scoring.. so please let me know if you hear something better! thanks ---------------------------------------------------------------------------------------------------------- You might like to consider Applied Biosystem's free software - Peak Scanner - available from their website. I've only just downloaded it so can't give you a verdict on its usefulness but I could rapidly input datafiles and see the peak traces. I haven't had much luck with STRand, particularly with the newer capillary equipment files. ---------------------------------------------------------------------------------------------------------- I highly recommend Genographer for AFLP analyses - I found it worked really well, and is free! Do keep in mind though that you have to run the raw ABI data through GeneScan (to define the ladder) before importing data into Genographer.... Sorry I can't offer microsat advice - I've always used GeneMapper.... --------------------------------------------------------------------------------------------------------- I recommend GeneMarker. I have used it extensively for AFLPs and I think that it has a very flexible set of tools and is very user-friendly. Also, support from SoftGenetics is quite nice. --------------------------------------------------------------------------------------------------------- I have used Strand for the past 2-3 years for my microsatellite work. It has worked fine for me and I opted to use it instead of the GeneMapper program. I have been pleased with the tech support when I have had questions and I have seen no down sides to using it. A colleague that was trying to learn both Strand and Genemapper said that he liked Strand's format better. That being said, I have not used the new fluorescent markers that ABI has recently developed and so I don't know how Strand behaves with them. Feel free to contact me if you have questions about Strand. ---------------------------------------------------------------------------------------------------------- I've used both Genemapper and now own GeneMarker, and can say without reservation that GeneMarker is excellent and worth every penny. The freeware just doesn't give you the flexibility and power that you get with GeneMarker, which, by the way, I'm using for both AFLPs and microsatellites. I should add that the support from SoftGenetics has been sine qua non, as well. ---------------------------------------------------------------------------------------------------------- I'd be grateful if you could send me any replies you get, or maybe post these on the evoldir list. I have only used GeneMapper (our lab has 1 copy) for analyzing microsatellite data. I have found it to be user-friendly and have no problems with the software, but I'd be very interested to hear about less pricey alternatives. ---------------------------------------------------------------------------------------------------------- -GeneMarker (SoftGenetics, LLC) Software is able to differ automatically between peaks with good and bad quality. Unfortunately, very often you don´t really know what the software does. Didn´t work for my data. Nice people at SoftGenetics, visit you at your lab to demonstrate the software. I think there´s a 30-days trial version available -STRand (UC Davis,http://www.vgl.ucdavis.edu/informatics/STRand/index.html) Don´t know that. -Genographer Just tested once. Couldn´t find a real difference between Genographer and the software of ABI. -Any others? Check out the software "Peakmatcher". It gives you a list of best categories based on repeatability of peaks you can use in Geneotyper (or Genemapper?). The software is free but i don´t find the webpage right know. But I can send the software by mail. Check out this review: "Statistical analysis of amplified fragment length polymorphism data: a toolbox for molecular ecologists and evolutionists" by Bonin et al. in Molecular Ecology, Vol. 16, No. 18, Sept,. 2007. It is a very helpful paper dealing with analysis of AFLPs including a list of software. The focus of the review is on statistical analysis of your data not on scoring. ---------------------------------------------------------------------------------------------------------- I was in similar situation earlier this year and decided to go for GeneMarker. And I'm quite happy with that. GeneMarker is capable of processing large number of samples, has automatic scoring option and allows manual editing. You can ask for a fully functional trial version (30days) and the technical support is very good. There are little things (with displaying, sorting, editing etc) that I would personally prefer to work differently, but they are planning some development on the software soon, so there might be some improvements soon. So can recommend :-) Bellow is a summary of responses I got from Evol Dir to my query. Good luck! Sarka 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 [EMAIL PROTECTED] 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 ----------------------------------------------------------------------------------------------------------
