Haplotype inference with pseudo-Boolean optimization

The fast development of sequencing techniques in the recent past has required an urgent development of efficient and accurate haplotype inference tools. Besides being a crucial issue in genetics, haplotype inference is also a challenging computational problem. Among others, pure parsimony is a viable modeling approach to solve the problem of haplotype inference and also an interesting NP-hard problem in itself. Recently, the introduction of SAT-based methods, including pseudo-Boolean optimization (PBO) methods, has produced very efficient solvers. This paper provides a detailed description of RPoly, a PBO approach for the haplotype inference by pure parsimony (HIPP) problem. Moreover, an extensive evaluation of existent HIPP solvers, on a comprehensive set of instances, confirms that RPoly is currently the most efficient and robust HIPP approach.