Apparently BayEnv is the way to do differentiation scans. Here I offer some scripts and advice to help the you use Bayenv.

Install, no problem get it here: Unzip.

I have to say the documentation is not very good.

There is 2 things you will probably want to use BayEnv for:
1) Environmental correlations
2) XtX population differentiation
I will just be showing XtX here. Both need a covariance matrix. This is not the “matrix.out” file you get from the matrix estimation step.
. But first the SNP table.

Here is a script Greg O made to make a “SNPSFILE”* for bayenv from our standard SNP table format: SNPtable2bayenv I’ve made a small modification so that it excludes any non-bi-allelic site and to also print out a loci info file.
Use it like this:

perl SNPfile POPfile SampleFile

This will make three files with “SampleFile” appended to the start of the name.
*not actually a SNP file at all, it is an allele count file.

Input SNPfile (all spaces are tabs):

chr1 378627 AA TT NN TT AA
chr2 378661 AA AG NN GG AA
chr3 378746 GG AA NN AA GG
chr4 383246 NN GG NN GG TT
chr5 397421 CC GG NN GG CC
chr6 397424 GG AA NN AA GG
chr7 409691 NN CC NN NN GG
chr8 547653 AA GG NN GG AA
chr9 608412 AA GG NN NN AA
chr10 756412 GG CC NN CC GG
chr11 1065242 NN TT NN NN CC
chr12 1107672 NN TT NN TT NN

POPfile (all spaces are tabs):

S1 p1
S2 p1
S3 p2
S4 p2

Now estimate the covarience matrix:

./bayenv2 -i SampleFile.bayenv.txt -p 2 -k 100000 -r21345 > matrix.out

Now this is “matrix.out” file is not what you actually want. You have to use it to make a new file that contains a single covariance matrix. You could use “tail -n3 matrix.out | head -n2 > CovMatrix” or just cut it out yourself. Currently I am just using the last (and hopefully converged) values.
My CovMatrix.txt looks like this (again single tabs between):

3.009807e-05 -1.147699e-07   
-1.147699e-07 2.981001e-05

You will also need a environment file. I am not doing the association analysis so am just using some fake data. It is one column for each population and each row is the environmental values. Tab separated.

1 2

Now you can do the population differentiation test for each snp using a “SNPFILE”. I bet you think you are ready to go? Not so fast, you need a “SNPFILE” not a “SNPSFILE”. Not that either actually really have SNPs in them, just allele counts. Not that I am bitter. SNPFILE is just one site from the SNPSFILE. Here is a script that takes your “SNPSFILE” and runs the XtX program on each of the sites: RunBayenvXtX

perl SampleFile.bayenv.txt SampleFile.LocInfo.txt CovMatrix.txt FakeEnv.txt 2 1 

Where 2 is the number of populations and 1 is the number of environmental variables.
This will produce a file that has the site, allelecountfile name and the XtX value.