Pool-HMM & Freq-HMM

This projects provides three related Python programs :

- Freq-hmm estimates the allele frequency spectrum and detects selective sweeps using allele frequency data for a sample of individuals from the same population. It implements the HMM method of Boitard et al (2009).

- Pool-hmm extends this approach to the use of NGS data obtained from pooled DNA. It estimates allele frequencies at each position from NGS data and accounts for the uncertainty of this estimation when computing the allele frequency spectrum and detecting sweeps. It implements the HMM method of Boitard et al (2012).

- Estim2freq collects the allele frequencies estimated independently by Pool-hmm or Freq_hmm for different populations aligned on the SAME reference genome and for a SINGLE chromosome or contig, into a single file with one column per population and one line per genomic position where allele frequency estimates have been obtained for ALL populations.

The latest version of these programs can be downloaded from the "Files" tab.
More details and documentation