Dear Evoldir users,

I sincerely apologize for the delay of this answer.

More than a month ago, I asked for tools that estimate FST index for each
locus for Genome wide data.

I am really grateful to all the users that answered me, providing a very
useful help.

First of all, let me say that Bruce Weir sent me an e mail suggesting me to
be cautious about single-SNP estimates, since the variances are too large.

Please find below the answers that I received. Please feel free to contact
me for every enquiry.

 Hi Francesco,

I used the hierfstat R package for analysis of 13 mio SNPs in 20
individuals. The variance component estimation might not be the fastest,
but once you get SNP-wise estimates, any kind of randomization is fast.

cheers,
Reto

Francesco,

The speed of the analysis will depend to a certain extent on your
computers processor and RAM, but I would recommend Fstat or Genalex.

Good luck,

Dan

Hi,

have you tried hierfstat (R package) and its function basic.stats (much
faster than varcomp.glob)

Dear Francesco,

Hierfstat or Plink should be able to do it.

Armando

Hi Francesco,

Read this post:
http://www.molecularecologist.com/2012/05/calculating-pair-wise-unbiased-fst-with-r/

I personally use the Rpackage "hierfstat" to calculate Fst for >200k SNPs
relatively quickly.

I have also used MSA in the past for medium size SNP datasets. It does the
same calculation as Hierfstat.

MSA reference:

Dieringer, D. and Schlötterer, C. (2003), microsatellite analyser (MSA): a
platform independent analysis tool for large microsatellite data sets.
Molecular Ecology Notes, 3: 167–169. doi: 10.1046/j.1471-8286.2003.00351.x

cheer,

sebastien

Dear Francesco,

We use here a software called ADEGENET (R-source) for large datasets
analyses (Gen Div, H&W, FST, Multivariate analyses).

I would be happy to hear what other suggestions you receive from the
community.

Sincerely,

Gregory

Dear Francesco,

we are developing 'PopGenome',  a powerful toolbox for population genetic &
genomic data within the R statistics environment (http://www.r-project.org/).
A substantially improved version 1.2 will be online at CRAN very soon - in
the meantime, I'd be happy to email you (or anyone else interested) the
package. It will run on Windows, MacOS, and Linux.

PopGenome implements a wide range of population genetics statistics and
methods, including different variants of F_ST. These can be applied to sets
of alignments, sets of loci within a large SNP file (e.g., 'gene' or 'exon'
regions specified in an annotation file) , or sliding windows.

At this time PopGenome can read in the following data formats:
Alignments: FASTA, PHYLIP, MAF, MEGA, NEXUS.
SNP data: SNP, VCF, HAPMAP (in particular files from the 1000/1001 genomes
projects)

You can also split large datasets in your own format into chunks and
convert them into R-objects, PopGenome will concatenate them internally.
This mechanism is well documented and will also be available on CRAN.

To ensure fast computation on a very large scale we implemented some R
specific bottlenecks in C++.

If you have any further questions on PopGenome and its usage, please ask!

Best wishes,

Bastian

Francesco Montinaro <francesco.montinaro@gmail.com>