Towards a practical O(n log n) phylogeny algorithm

Recently, we have identified a randomized quartet phylogeny algorithm that has O(n log n) runtime with high probability, which is asymptotically optimal. Our algorithm has high probability of returning the correct phylogeny when quartet errors are independent and occur with known probability, and when the algorithm uses a guide tree on O(log log n) taxa that is correct with high probability. In practice, none of these assumptions is correct: quartet errors are positively correlated and occur with unknown probability, and the guide tree is often error prone. Here, we bring our work out of the purely theoretical setting. We present a variety of extensions which, while only slowing the algorithm down by a constant factor, make its performance nearly comparable to that of neighbour-joining, which requires ?(n3) runtime in existing implementations. Our results suggest a new direction for quartet-based phylogenetic reconstruction that may yield striking speed ! improvements at minimal accuracy cost. An early prototype implementation of our software is available at http://www.cs.uwaterloo.ca/~jmtruszk/qtree.tar.gz.