I have a set 680k SNP for 141 individuals. Can anyone suggest a software to detect selection?
At the moment I am looking at gpat++ and rehh. Both of them require to specify a region, chromosome and position e.g. 1-1000 for gpat++ and chromosome for rehh (only ~1500 SNPs per chromosome in example). Are there any programs which allow to calculate e.g. iHS for a whole chromosome with large number of SNPs?