Hi, I am having trouble on data analysis for SSR markers in Popgene Software.
My data:
100 populations ( 3 replicates each)
20 SSR markers (2-12 bands/allele each)
I scored them in binary format and prefer analysis on this format. I converted my file from GenAlEx to Popgene format.
It worked as a dominant, haploid marker but not as a co-dominant, haploid marker wherein an error is encountered (as in attached screenshot).
However, my problem, same as in GenAlEx is that, I cannot analyze considering each locus/band/allele within an SSR marker (as mentioned, I have 2-12 alleles for each). The programs only consider each bands within SSR locus as a single band/locus. What shall be the proper formatting? Can you attach a simple input file format for each program?
Thank you!
Hi precious,
couldnt you do it as I proposed here ?
https://www.researchgate.net/post/How_can_I_coding_microsatellite_SSR_data_into_0_1_2_format
You can try with software like Powermarker (its a free software and very good). There is also a software called Arlequin which may be usefull for you (but I prefer powermarker). In GenAlEx you shoud try changing the name of each locus/band/allele within an SSR marker for a different one - that way you can analyze them separately.
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