A Faster Construction of Greedy Consensus Trees

Abstract

A consensus tree is a phylogenetic tree that captures the similarity between a set of conflicting phylogenetic trees. The problem of computing a consensus tree is a major step in phylogenetic tree reconstruction. It also finds applications in predicting a species tree from a set of gene trees. This paper focuses on two of the most well-known and widely used oconsensus tree methods: the greedy consensus tree and the frequency difference consensus tree. Given $k$ conflicting trees each with $n$ leaves, the previous fastest algorithms for these problems were $O(k n^2)$ for the greedy consensus tree [J. ACM 2016] and $\tilde O(\min \{ k n^2, k^2n\})$ for the frequency difference consensus tree [ACM TCBB 2016]. We improve these running times to $\tilde O(k n^{1.5})$ and $\tilde O(k n)$ respectively.