Hi, I have problems to get a SNP input file working well in Genalex. I tried to change letters by numbers (A=1; C=2; G=3 and T=4) in one column but it does not work. It does not seem to work either using numbers and two columns (codominant). Some help on that ?? In attached, an exemple of my SNP data set. Thanks
Dear Severine
I have coded the first two loci for you in the attached file. But, please note there is some header files you will need to fill. Please take a look at the manual
Hope this helps
Pablo
Hi, many thanks for your reply ! I think the problem is that Genalex is OK for PCA approaches using SNPs data, but it can't do relatedness calculations. Have you tried to calculate relatedness ?
Hi Severine
I have worked with SSRs and usually recommend Spagedi. You can check it here http://ebe.ulb.ac.be/ebe/SPAGeDi.html.
.Pablo
Not sure, but I can not see any reason why not. Anyhow, checking it on the manual shouldn't take you a long time
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