Simple but Fundamental Limitations on Supertree and Consensus Tree Methods

Simple but fundamental limitations on supertree and consensus tree methods.

Polynomial Supertree Methods Revisited

Supertree methods allow to reconstruct large phylogenetic trees by combining smaller trees with overlapping leaf sets into one, more comprehensive supertree. The most commonly used supertree method, matrix representation with parsimony (MRP), produces accurate supertrees but is rather slow due to the underlying hard optimization problem. In this paper, we present an extensive simulation study c...

Polynomial Supertree Methods in Phylogenomics

One of the objectives in modern biology, especially phylogenetics, is to build larger clades of the Tree of Life. Large-scale phylogenetic analysis involves several serious challenges. The aim of this thesis is to contribute to some of the open problems in this context: Perhaps most important in general is the design of fast and efficient algorithms to reconstruct large phylogenetic trees. In o...

Performance study of supertree methods

INTRODUCTION Phylogenetic trees depict the relationships among varying species [1]. A simple example of this is a family tree. When referring to Figure 1, the three most important components of a tree include: the Node(s) (denoted by squares), the Branches (denoted by lines), and the Tips (denoted by circles). The Nodes represent the hypothetical ancestors. The Branches represent the evolution ...

Supertree methods for building the tree of life: divide-and-conquer approaches to large phylogenetic problems