Phylogenetic Trees

Abstract

This chapter discusses a Steiner tree problem in biology. The chapter reviews various approaches to codifying this problem and various algorithms for these approaches. There are several types of phylogenetic trees that can only be described as “the tree this algorithm builds.” While a phylogenetic tree is inherently rooted, due to the historical nature of evolution, it is common to define unrooted phylogenetic trees, which specify the branching topology but do not suggest where in the tree the root is found (due to a lack of evidence). It is also convenient to work with unrooted trees when using an approach that exhausts all topologies, because there are fewer of them. It is fundamental to any Steiner problem, including phylogenetic trees, that there is a notion of distance. When the points are in some metric space the distance are well-defined. The chapter also discusses computational complexity results. Later, algorithms are presented for the various formulations. © 1992, Elsevier Inc. All rights reserved.