ASTRAL: genome-scale coalescent-based species tree estimation

Species trees provide insight into basic biology, including the mechanisms of evolution and how it modifies biomolecular function and structure, biodiversity and co-evolution between genes and species. Yet, gene trees often differ from species trees, creating challenges to species tree estimation. One of the most frequent causes for conflicting topologies between gene trees and species trees is incomplete lineage sorting (ILS), which is modelled by the multi-species coalescent. While many methods have been developed to estimate species trees from multiple genes, some which have statistical guarantees under the multi-species coalescent model, existing methods are too computationally intensive for use with genome-scale analyses or have been shown to have poor accuracy under some realistic conditions. Results: We present ASTRAL, a fast method for estimating species trees from multiple genes. ASTRAL is statistically consistent, can run on datasets with thousands of genes and has outstanding..., Availability and implementation: ASTRAL is available in open source form at https://github.com/smirarab/ASTRAL/. Datasets studied in this article are available at http://www.cs.utexas.edu/users/phylo/datasets/astral. Contact: Â [e-mail] Supplementary information: Â Supplementary data are available at Bioinformatics online., , # ASTRAL: genome-scale coalescent-based species tree estimation This repository includes both simulated and biological dataset. ## Description of the data and file structure The following datasets are used in the ASTRAL paper shown above. All these archive files include README files that describe their content. ### biological.zip: This file includes: 1\. our estimated gene trees on alignments provided to us by authors of Song et al, 2012, PNAS, 2\. our estimated species trees on the same dataset. We have re-analyses of two biological datasets in our paper. #### Song et al dataset We obtained gene alignments from the Song et al and re-estimated gene trees and species trees. The following files are included in mammals.zip * mammals-alignments.zip contains all the alignments that we obtained from Song et al. * mammals-genetreess.zip contains gene trees that we estimated. For each gene, we include 3 files * RAxML_bipartitions.final.f200 is the bestML tree with support...