Dear all,
I would appreciate your help in getting the script on R with regards to count the private alleles number and frequency per location. I am working on the genetic diversity and population structure of isolates of Zymoseptoria tritici on wheat that were collected from different locations in Tunisia.
Thank you,
Hey Rim
Sorry, I don't have an r-script for it but I have been using an excel plugin for it.
Here is the link for it https://biology-assets.anu.edu.au/GenAlEx/Download.html
It calculates various diversity indexes and is quite easy to use.
Hi Rim,
e.g. the package strataG provides both using the calls "privateAlleles" and "alleleFreqs". But make sure you format your genind object or whatever you used to gtype class. Hope this helps, cheers, Christoph
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