Locating recombination hot spots in genomic sequences through the singular value decomposition

Locating recombination hotspots in genomic data is an important but difficult task. Current methods frequently rely on estimating complicated models at high computational cost. In this paper we develop an extremely fast, scalable method for inferring recombination hot spots in a population of genomic sequences that is based on the singular value decomposition. Our method performs well in several synthetic data scenarios. We also apply our technique to a real data investigation of the evolution of drug therapy resistance in a population of HIV genomic sequences. Finally, we compare our method both on real and simulated data to a state of the art algorithm.