We present a new, statistically consistent algorithm for phylogenetic tree construction that uses the algebraic theory of statistical models (as developed in Chapters 1 and 3). Our basic tool is Singular Value Decomposition (SVD) from numerical linear algebra.

Starting with an alignment of n DNA sequences, we show that SVD allows us to quickly decide whether a split of the taxa occurs in their phylogenetic tree, assuming only that evolution follows a tree Markov model. Using this fact, we have developed an algorithm to construct a phylogenetic tree by computing only O(n2) SVDs.

We have implemented this algorithm using the SVDLIBC library (available at http://tedlab.mit.edu/~dr/SVDLIBC/) and have done extensive testing with simulated and real data. The algorithm is fast in practice on trees with 20–30 taxa.

We begin by describing the general Markov model and then show how to flatten the joint probability distribution along a partition of the leaves in the tree. We give rank conditions for the resulting matrix; most notably, we give a set of new rank conditions that are satisfied by non-splits in the tree. Armed with these rank conditions, we present the tree-building algorithm, using SVD to calculate how close a matrix is to a certain rank. Finally, we give experimental results on the behavior of the algorithm with both simulated and real-life (ENCODE) data.

The general Markov model

We assume that evolution follows a tree Markov model, as introduced in Section 1.4, with evolution acting independently at different sites of the genome.