Phylogenetic tree distance computation over succinct representations

Abstract

There are several tools available to infer phylogenetic trees, which depict the evolutionary relationships among biological entities such as viral and bacterial strains in infectious outbreaks, or cancerous cells in tumor progression trees. These tools rely on several inference methods available to produce phylogenetic trees, with resulting trees not being unique. Thus, methods for comparing phylogenies that are capable of revealing where two phylogenetic trees agree or differ are required. An approach is then to compute a similarity or dissimilarity measure between trees, with the Robinson- Foulds distance being one of the most used, and which can be computed in linear time and space. Nevertheless, given the large and increasing volume of phylogenetic data, phylogenetic trees are becoming very large with hundreds of thousands of leafs. In this context, space requirements become an issue both while computing tree distances and while storing trees. We propose then an efficient implementation of the Robinson-Foulds distance over trees succinct representations. Our implementation generalizes also the Robinson-Foulds distances to labelled phylogenetic trees, i.e., trees containing labels on all nodes, instead of only on leaves. Experimental results show that we are able to still achieve linear time while requiring less space. Our implementation is available as an open-source tool at https://github.com/pedroparedesbranco/TreeDiff.