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  and the other proposed by Saitou and Nei . 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 evaluating phylogenetic trees is then transformed into the standard linear least squares problem. Then we propose a matrix decomposition method for evaluating phylogenetic trees.
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