Format

Send to

Choose Destination
Bioinformatics. 2015 Jun 15;31(12):i44-52. doi: 10.1093/bioinformatics/btv234.

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

Author information

1
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.

Abstract

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 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.

AVAILABILITY AND IMPLEMENTATION:

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/.

CONTACT:

smirarab@gmail.com

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
26072508
PMCID:
PMC4765870
DOI:
10.1093/bioinformatics/btv234
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Silverchair Information Systems Icon for PubMed Central
Loading ...
Support Center