A covariance matrix inversion problem arising from the construction of phylogenetic trees

Abstract: The authors of this paper describe an efficient algorithm for the inversion of covariance matrices that arise in the context of phylogenetic tree construction. Phylogenetic trees describe the evolutionary relationships between species, and their construction is computationally demanding. Many approaches involve the symmetric matrix of evolutionary distances between species. Regarding these distances as random variables, the corresponding set of variances and covariances form a rank-4 tensor, and the inner-product defined by its inverse can be used to assign statistical scores to candidate trees. The paper describes a natural set of assumptions for the phylogenetic tree under construction, and shows how under these assumptions the covariance tensor for a tree with n leaves can be inverted in O(n²) operations. In addition to presenting the inversion algorithm, the authors hope that this article will open algebraic and computational problems from the field of phylogeny to a wider audience.