Evaluating Phylogenetic Trees by Matrix Decomposition.

Evaluating Phylogenetic Trees by Matrix Decomposition

A Matrix Representation of Phylogenetic Trees

In this paper we begin by describing two currently used methods for evaluating phylogenetic trees, one proposed by Fitch and Margoliash 5] and the other proposed by Saitou and Nei 7]. Both methods are heuristic in the sense that not all possible trees are tested to ensure that the best solution has been reached. We develop a matrix representation of unrooted binary trees. The problem of evaluat...

Computational Tools for Evaluating Phylogenetic and Hierarchical Clustering Trees

Inferential summaries of tree estimates are useful in the setting of evolutionary biology, where phylogenetic trees have been built from DNA data since the 1960’s. In bioinformatics, psychometrics and data mining, hierarchical clustering techniques output the same mathematical objects, and practitioners have similar questions about the stability and ‘generalizability’ of these summaries. This p...

Development of New Methods for Inferring and Evaluating Phylogenetic Trees

A Steiner Tree, Substitution Matrix Method for Reconstructing Phylogenetic Trees

Evolutionary theory implies that existing or extinct organisms are descended from a common ancestor. Hence, given a set of organisms, a phylogenetic tree can be reconstructed showing the evolutionary relationships between the biological organisms in the set. A commonly used method for the reconstruction of phylogenetic trees is the Distance Matrix (DM) method, which tends to be faster than the ...