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++](https://github.com/jewmanchue/vcflib/wiki) and [rehh](http://cran.r-project.org/web/packages/rehh/index.html). 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?
There's a new, very user friendly implementation of most EHH test that you might be interested in.

Here's the link: https://github.com/szpiech/selscan

From the manual:

> 
> ```
> selscan -- a program to calculate EHH-based scans for positive selection in 
>	genomes
>
> Copyright (C) 2014  Zachary A Szpiech
> 
> selscan currently implements EHH, iHS, and XP-EHH, and requires phased data. 
> It should be run separately for each chromosome and population (or population 
> pair for XP-EHH).  selscan is 'dumb' with respect ancestral/derived coding and
> simply expects haplotype data to be coded 0/1.  Unstandardized iHS scores are 
> thus reported as ln(iHH1/iHH0) based on the coding you have provided.
> ```