Help me Please.
I'm working on rice varieties diversity and I'd like to use GenAlex software for analysis (Na, Ne, Ho, He, I, F,PIC, AMOVA, etc). Data were get from DArT. Those data are coded as 0 for reference allele homozygote, 1 for SNP allele homozygote and 2 for heterozygote. So, should I format the following data as Codominant (two columns per locus) or haploid (one colomn per locus) GenAlex? In case of codominant, how could I present heterozygote data?
Regards!
Hi Erum,
I am having the same difficulty, but I cannot get the export of a distance matrix to be recognized by Mega. I just clicked export —> Mega and left options as defaults. I am concerned because I have made a distance matrix from within GenAlEx (using microsatellite chromat scored as integers—other analyses have worked fine) but the export dialogue box doesn’t offer ‘codominant’ as an option; it seems to only offer ‘sequence data’ as an option.
Hello,
Were you able to solve this problem? Please share your success. I am trying to solve the same problem and i need your help.
Regards
Hi, I feel like a lot of time has passed since this question has been asked but for what it's worth, if you have data from Diversity Arrays like Zaki, the easiest way is to your the dartR package, transform the genlight object to genind and then export the data via gi2genalex.
If you follow the dartR package a transform your data to gening object in
R, the you can use the function genind2genalex from poppr https://rdrr.io/cran/poppr/man/genind2genalex.html
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