Fixed topology alignment with recombination Original Research Article

In this paper, we study a new version of multiple sequence alignment, fixed topology alignment with recombination. We show that it cannot be approximated within any constant ratio unless P=NP. For a restricted version, we show that the problem is MAX-SNP-hard. This implies that there is no PTAS for this version unless P=NP. We also propose approximation algorithms for a special case, where each internal node has at most one recombination child and any two merge paths for different recombination nodes do not share any common node.