InferRho2

InferRho2 is a MCMC based program that jointly estimates 3 recombination parameters, the population crossing-over rate, the population gene-conversion rate and the mean conversion tract length from population genomic datasets under a Bayesian framework. It uses a full-likelihood method to infer the posterior distribution of recombination rates along the sequence under a variable recombination rate model that includes hotspots. The ratio of gene-conversion to crossing-over rates can take 2 possible values f1 and f2 within hotspots and non-hotspots respectively.

The program outputs the posterior distribution of f1, f2 and the 3 recombination parameters for marker intervals in the .rho output files.

Starts, Ends and Intensities of hotspots are output in the .hotsp output files.

We suggest omitting SNPs with minor allele frequency < 10% and applying the program to short windows in your dataset (e.g. 5-7 kb).