ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes

MOTIVATION: The estimation of species phylogenies requires multiple loci, since different loci can have different trees due to incomplete lineage sorting, modeled by the multi-species coalescent model. We recently developed a coalescent-based method, ASTRAL, which is statistically consistent under the multi-species coalescent model and which is more accurate than other coalescent-based methods on the datasets we examined. ASTRAL runs in polynomial time, by constraining the search space using a set of allowed 'bipartitions'. Despite the limitation to allowed bipartitions, ASTRAL is statistically consistent. RESULTS: We present a new version of ASTRAL, which we call ASTRAL-II. We show that ASTRAL-II has…

• NS
  National Science Foundation

  Awards: 1062335, 0733029
• HH
  Howard Hughes Medical Institute