<p>Hi!</p>

<p>I have ped/map file containing two populations (~110 samples, ~500k SNPs). Is there a software which can phase the data? Alleles should be coded as 1 and 0, where 0 reflects ancestral allele.</p>

<p>I am trying to detect selection and at the moment preparing an input file for <a href="https://github.com/szpiech/selscan">selscan</a> programm. So if you can suggest good alternative programs it will help as well.</p>

<p>Thanks.</p>

Was the data in VCF format before plink? There are lots of ways to phase in VCF. BEAGLE is my preferred phasing algorithm.

Also if your are interested, I have been writing selection software that works directly from VCF.

https://github.com/jewmanchue/vcflib/wiki