I would like to have an alternative for AppliedBiosystems microsatellite fragment analysis (genotyping) software GeneMapper as I want to be able to work at home. What would be your suggestions for a free downloadable alternative or demo version for at least 30 days? Peak Scanner doesn't have genotyping function so I don't like it at all as I work with polyploids.
Alberto, I was not, nevertheless I used 2 different PCs at home (not mine, borrowed) each for 30 days with GeneMapper 5.0 demo version (freely available online at lifetechnologies website after registration). That's how I solved this problem. But if I had to use GeneMapper again, I would have to find one more new PC, as my demo versions on previous PCs already passed 30 day deadline :(
Dear Asta,
I highly recommend Geneious http://geneious.com/ It has a free 30 day trial, and the microsatellite plug-in is fantastic. I have used it for all of my microsatellite analyses and have been very happy with it. Please feel free to e-mail me if you run into any problems, and I'll do my best to help you.
Jeremy
Dear Jeremy, was thinking about Geneious at that time, but never tried it, as back then was short of time to learn smth new and was already familiar with GeneMapper, but now I think will follow your suggestion, thank you.
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What version of gene mapper did you use? I have tried the version 5 but although I tried different PC computer, none of them were powerful enought to run the program. I am trying to get nice chromatogram to publish but I can find a good program for mac. I will give a try with geneious!!!
I used GM ver 4, installed on lab PC (XP Win).....
but ver 5 worked fine on Win 7 at home with standard pc's, I'm in doubt how gene mapper can help you with chromatogram unless you know it can. If you can -try Geneious instead GM.
Can't believe it has been over a year since replying to this post, but I would also recommend Geneious Software with the microsat plugin. It is very intuitive and user-friendly.
Hi Asta I recommend GeneMarker It has a free 90 day trial. good luck!
Peak Scanner free cloud version is now available from Thermo Fisher. It is easy to use, for both Mac and PC. You can get further (secondary analysis) from https://www.fragmentanalysis.com.
I would recommend, GeneMarker. Demo for 30 is freely available and it will serve your purpose.
The microsatellite plugin in Geneious is fantastic! Geneious is user friendly, can be used on a Mac, as well as Windows and Linux, and looks nice. I initially tried Peakscanner because it was free, but it put each allele on it's own row rather than each locus being a row, which is incredibly user-unfriendly. Geneious is also much, much cheaper than GeneMapper from what I recall. You can specify the size ranges for each locus, genotype multiple loci per run, bin your calls based on the size of the repeat, and it will mark the peaks automatically so you just have to scroll through and fix any mistakes. I was using Geneious R8 with the plugin, but I don't think the plugin has changed in newer versions. I didn't have convenient access to GeneMapper as a graduate student, and used a Mac, so Geneious was a lifesaver.
Hi all, I think Fragman (an R package) freely available works great. I've used it recently and I can't complain.. even though not really user friendly
I came across this git repo, written in python, that says it largely performs the same functions as GeneMapper:
https://github.com/trmznt/fatools
I have not personally used this but plan to in the near future. If you try it before me and have any advice, I'll be happy to hear it.
NCBI has released Windows and Macintosh versions of OSIRIS software that will do fragment analysis of .FSA or .HID files. Analyzes 2-5 channels of data allowing multiplexing. Free and open source download from: https://www.ncbi.nlm.nih.gov/osiris/ https://www.ncbi.nlm.nih.gov/osiris/new/
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