title: ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes.
abstract: BACKGROUND
  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 substantial advantages over ASTRAL: it is faster, can analyze much larger datasets (up to 1000 species and 1000 genes) and has substantially better accuracy under some conditions. ASTRAL's running time is [Formula: see text], and ASTRAL-II's running time is [Formula: see text], where n is the number of species, k is the number of loci and X is the set of allowed bipartitions for the search space.
  
  
  METHODS
  ASTRAL-II is available in open source at https://github.com/smirarab/ASTRAL and datasets used are available at http://www.cs.utexas.edu/~phylo/datasets/astral2/.
  
  
  BACKGROUND
  smirarab@gmail.com
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Computer Science, The University of Texas at Austin, Austin, TX 78712, USA and Departments of Computer Science and Bioengineering, The University of Illinois at Urbana-Champaign, Champaign, IL 61801, USA.
authors.forename: Siavash
authors.initials: S
authors.lastname: Mirarab
authors.affiliation: Department of Computer Science, The University of Texas at Austin, Austin, TX 78712, USA and Departments of Computer Science and Bioengineering, The University of Illinois at Urbana-Champaign, Champaign, IL 61801, USA.
authors.forename: Tandy
authors.initials: T
authors.lastname: Warnow
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D003627:Data Interpretation, Statistical; D017343:Genes, Plant; D049810:Genetic Speciation; D023281:Genomics; D010802:Phylogeny; D010944:Plants / Q000145:classification* / Q000235:genetics*