A more efficient approximation scheme for tree alignment

We present a new polynomial time approximation scheme (PTAS) for tree alignment, which is an important variant of multiple sequence alignment. As in the existing PTASs in the literature, the basic approach of our algorithm is to partition the given tree into overlapping components of a constant size and then apply local optimization on each such component. But the new algorithm uses a clever partitioning strategy and achieves a better efficiency for the same performance ratio.

• Type: Conference
• Year: 1997
• Where: RECOMB
• Authors: Lusheng Wang, Tao Jiang, Dan Gusfield
• Keywords: Computational Biology, Multiple Sequence Alignment, Polynomial Time Approximation Scheme, RECOMB 1997, Tree Alignment