If we want to study the population genetics/population structure of 30 genotypes by employing SSR markers. How we have to prepare input data file of SSR markers data to analyse in POPGENE Software.
Useful docs for that:
POPGENE manual
https://sites.ualberta.ca/~fyeh/popgene.pdf
PGDSpider (Software for convertion between genetic/genomic data types)
http://cmpg.unibe.ch/software/PGDSpider/PGDSpider%20manual_vers%202-0-1-9.pdf
GenAlex (Genetic Analysis in Excel)
https://biology-assets.anu.edu.au/GenAlEx/Welcome.html
Best
Required one,
1. you have to mention No. of Population, and No. of Loci (primers)
2. you have maintain primer scoring in diploid state.
3. use specific input Language to maintain specificity
* for your reference i am attaching screen shot go through that. Good Luck.
suggestion.
instead of POPGENE, use can use GenAlEx for SSR data analysis and visualization, for structure use STRUCTURE.
Consideration- GenAlEx and STRUCTURE uses scoring input based on Weightage of Band
Mahammed Faizan thank you very much for the reply.
Whether GenAlEx will work if I have got multiple bands for same primer.
No, Nagaraja N R Sir' you have to consider 2 bands.
if you want to consider multiple bands you have to go for NTSYS or Darwin Software
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