Best tool for Fst calculation with over a thousand SNP among 6 populations??

Question

[su7880]

Hello,

What tools are you guys using to calculate Fst? I tried Arlequin, Genalex etc. They all are good for over all summary. The problem with the software above was that I couldn't have a mean pairwise Fst value between 6 pops for each 1600 SNP loci. Presumably, those 6 pops are composed of two species i.e. three for each species. I need to look at Fst value for each loci then determine the loci that are diagnostic for species identification using Fst as a cutoff.
I tried R packages but my personal cp doesn't have enough memory to handle it.

Thank you in advance.

Answer 1

[JstRoRR]

Have a look at Popoolation2 and SelectionTools

[Adrian Pelin]

I have experienced Popoolation2 before, works great, make sure coverage is about 100. Also i learned recently of another tool: https://github.com/hugheslab/snpgenie