A Faster Construction of Phylogenetic Consensus Trees

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 consensus 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 Opknq for the greedy consensus tree [J. ACM 2016] and Õpmintkn, knuq for the frequency difference consensus tree [ACM TCBB 2016]. We improve these running times to Õpknq and Õpknq respectively. ar X iv :1 70 5. 10 54 8v 2 [ cs .D S] 4 J ul 2 01 7