I'm trying to do genetic analysis (allele frequency, polymorphic informative content, Shannon and Nei's index, etc) and acording to a paper, they used the program Popgene 1.32v with their SSR converted to 1= presence, and 0= absence of band. Ok, I converted my data into a binary matrix(excel: rows are individuals and columns the different loci), separated the data into 4 populations acording the quick user's guide and no matter what it keeps presenting this box: "RAPD data has to be 0 or 1. '.' is used to indicate the missing value. Check population 3 locus 1"
In pop.3 locus 1 is a column filled with 0 por that population. In the example file it also has a column with 0.
I don't understand what's wrong.
By the way, I'm analysing this data has a diploid dominant marker
Thank you all
Best regards
María Gabriela
Hi Maria,
You should consider SSR data as codominant markers (not dominant) during data analysis. please try that. Hope it works
Hi Mohamed. I can't use SSR data like codominant because is tetraploid data. I don't know how to write the data file, example: most data are like diploid but some have 4 different alleles! The program doesn't accept tetraploid data; the example in the manual was only for diploid.
Any advice?
Thank you
Thank you Huseyin!, I'm looking at genetic diversity papers in tetraploid populations with SSR, each one used a different program.
I'll check POLYSAT and let you know ^^
Hello everyone
I tried to use the programs you've recommended , but I must say I finally used GenAlex, converting my data into a binary matrix. POLYSAT didn't give much help, specially with the "partial heterozygous" (three alleles, how do I genotype it?)
Anyway, thank you for your advices
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