I have some (about 500 samples) NGS resequencing data (>100x coverage) of a few regions (Illumina reads 2x100bp). Now I want to do several things: 1. Haplotype phasing (-> assign haplotypes and which variants are on which haplotype etc.) 2. See whether there has been a positive selection for haplotypes during human evolution 3. Estimate the age of the identified haplotypes
Does anyone has experience with these analyses and can point me to which software I should use?