Asteroid: a new minimum balanced evolution supertree algorithm robust to missing data

Abstract

Motivation: Missing data and incomplete lineage sorting are two major obstacles to accurate species tree inference. Gene tree methods such as ASTRAL and ASTRID have been developed to account for incomplete lineage sorting. However, they can be severely affected by high levels of missing data. Results: We present Asteroid, a novel supertree method that infers an unrooted species tree from a set of unrooted gene trees. We show on both empirical and simulated datasets that Asteroid is more robust to missing data than ASTRAL and ASTRID, while being several orders of magnitude faster than ASTRAL for datasets that contain thousands of genes. Asteroid offers advanced features such as parallelization, support value computation, and support for multi-copy and multifurcating gene trees. Availability: Asteroid is freely available at \https://github.com/BenoitMorel/Asteroid