Question: Best tool for Fst calculation with over a thousand SNP among 6 populations??
0
gravatar for su7880
3.0 years ago by
su78800
su78800 wrote:

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.

snp • 2.4k views
ADD COMMENTlink modified 3.0 years ago by JstRoRR60 • written 3.0 years ago by su78800
1
gravatar for JstRoRR
3.0 years ago by
JstRoRR60
Germany
JstRoRR60 wrote:

Have a look at Popoolation2 and SelectionTools

ADD COMMENTlink written 3.0 years ago by JstRoRR60

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

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by Adrian Pelin2.2k
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