Selecting the branches for an evolutionary tree.: A polynomial time approximation scheme

Many fundamental questions in evolution remain unresolved despite the abundance of genetic sequence data that is now available. This state of affairs is partly due to the lack of simultaneously efficient and accurate computational methods for inferring evolutionary trees. Efficient methods are critical since the abundance of sequence data has resulted in the need to analyze large datasets. Methods with guaranteed accuracy are important since biologists require proof that results are meaningful. In this paper the first polynomial time approximation scheme (PTAS) for selecting the branches of an evolutionary trees from a list of candidate branches is presented. PTAS’s are highly desirable since they allow the approximation of an optimal solution with arbitrary precision in polynomial time. This PTAS is based upon recent advances in the approximation of smooth polynomial integer programs.  2003 Elsevier Inc. All rights reserved.