Other: Genographer.software.ANSWERS Hi, Evol-Dir, Here is my original post... Hi Evol-Dir, I would like to use the program Genographer to analyze fluorescent AFLP data using 5 dyes (6FAM, VIC, NED, PET, and the size standard LIZ) run on an ABI 3730 machine. The latest version of Genographer http://hordeum.oscs.montana.edu/genographer/ does not recognize the LIZ (orange) dye, and thus cannot be used for data with more than 4 dyes. A Google search brought up an abstract (http://www.intl-pag.org/13/abstracts/PAG13_P229.html ) regarding a modification to the software that would allow analysis of this data, however I have not had any luck with follow up emails to the abstract authors or to other colleagues. If anyone has written a modification to update Genographer and is willing to share it, or knows who to contact, please let me know. Thanks for your help, Heidi ..And here are the two relevant emails I received in response to this (see below). The "unofficial" update to Genographer does exist (see email #1 below from Ben Sikes) however it requires yet another program that is no longer supported as an intermediary (GeneScan). The other response (see email #2 below from Walter Durka) was a bit more promising, as it appears that Travis Blake is in fact developing a new version of Genographer that will import fluorescent AFLP profiles directly without having to use GeneScan. Genographer 2.0 can be downloaded now, but it is apparently not working on data with 5 dyes (yet). A number of other emails suggested other programs I might try for scoring AFLPs (including PeakScanner, a new free program from ABI: www.appliedbiosystems.com/PeakScanner ). For those interested, we have outlined a number of AFLP programs in Table 1 of a recent paper: Meudt, HM & AC Clarke. 2007. Almost Forgotten or Latest Practice? AFLP applications, analyses and advances. Trends in Plant Science 12(3):106-117. doi:10.1016/j.tplants.2007.02.001 Cheers, Heidi (Responses Below) Email #1 >From Ben Sikes [bensikes@gmail.com] I had a similar problem and did manage to get in contact with the guys who wrote that abstract. They gave me this message and the conversions worked fine on Genographer. Unfortunately the problem was that the 3730 files go straight into Genemapper and then are not usable in Genographer as it uses the Genescan data. In the end everyone in our groups has been 'pigeon-holed' into using Genemapper because ABI has monopolized how their data can be used... at least for now. Sorry for the bad news and I hope this helps. Sincerely, Ben On 11/18/06, Keenan Amundsen > wrote: Ben, There has not been an official update to Genographer, so we haven't made the changes available for download, but I am more than happy to send you what I have along with instructions for updating the "rusty" version. The program still relies on preprocessing data through GeneScan. ABI does not support this, but it can be done. Additionally there is a slight change in what I am sending you in that another researcher from Europe has had success in using newer versions of GeneScan to analyze her data. Also, let me know if you are working on a Mac instead of a PC and I can send those files instead. This is an e-mail that I've sent out before: There has been quite a bit of interest since PAG regarding the upgrades to Genographer and I'm happy to send you the modifications to update your version. There has not been an official upgrade to genographer and I'm not sure that there will be until some of the bugs are worked out, but hopefully these modification will get you by. Please open and read the file " TemporaryGenographerInstructions.doc"; it is a description of the modifications and file import process. If you would like a look at the *.java files I am more than happy to send those as well. Let me know if you have any trouble downloading the attachments and I can resend them. Keep in mind that we have only had success using an older version of GeneScan (version 3.1.2) to analyze the files before importing into genographer. The genographer modifications should allow for file import from GeneScan 3.5 and 3.7 analyzed files, but I have been having trouble getting those newer Genescan versions to size the DNA fragments. The new versions of GeneMapper (3.7) from ABI does support AFLPs but Genographer can not import GeneMapper files. Feel free to contact me with any questions. Also please let me know if you were successful in getting the changes to run and which versions of software (Genescan) you are using. Regards, Keenan Keenan Amundsen Plant Biology Research Tech. Floral and Nursery Plants Research Unit Rm. 118, Bldg. 010A, BARC-West 10300 Baltimore Avenue Beltsville, MD 20705-2350 Phone: 301-504-5469 ext. 235 Fax: 301-504-5096 http://www.usna.usda.gov/ Please Note New E-mail: keenan.amundsen@ars.usda.gov Also if you have problems responding to an e-mail that I have sent you, check to see (and remove) if there are extra domain extensions on my address (.local and arsnet. are common), since this will prevent a response. Email #2 >From Walter Durka [walter.durka@ufz.de] Hi there is a newly developed Genographer 2 (http://sourceforge.net/projects/genographer) which reads ABI3100 data. This verion is made by Travis Banks. It can read the five dyes; but at the moment does not correctly interprete the LIZ size standard (but try, perhaps it works with your data). I am in contact with Travis for some weeks now to solve this problem. His last mail said that he will have a new version these days.... regards Walter Heidi M. Meudt, Ph.D. Research Scientist, Botany Museum of New Zealand Te Papa Tongarewa P.O. Box 467 Wellington New Zealand heidim@tepapa.govt.nz phone: +64 4 381 7127 fax: +64 4 381 7070 website: http://www.tepapa.govt.nz/TePapa/English/CollectionsAndResearch/ResearchAtTepapa/Projects/Plants/ -and- Adjunct Research Associate School of Biological Sciences Victoria University 1-85 Kelburn Parade Room 507, New Kirk Building Wellington New Zealand phone: +64 4 463 5026 fax: +64 4 463 5331 website: http://www.vuw.ac.nz/sbs/staff/staff_research_fellows/meudt-heidi/meudt-heidi.aspx HeidiM@tepapa.govt.nz