ASTRAL-II swMATH ID: 20492 Software Authors: S. Mirarab, T. Warnow Description: 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 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 O(n2k∣∣X∣∣2), and ASTRAL-II’s running time is O(nk|X|2). , 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 Homepage: https://github.com/smirarab/ASTRAL Source Code: https://github.com/smirarab/ASTRAL Related Software: ASTRID; STEM-hy; FastTree; RAxML; BEAST; Quartets MaxCut; OCTAL; BUCKy; FastMe; MrBayes; ape; PhyloNet; DEPP; SimPhy; DendroPy; Seq-Gen; PAUP*; Phylo-MCOA; APPLES; PhyloGeoTool Cited in: 22 Publications all top 5 Cited by 40 Authors 4 Warnow, Tandy J. 3 Kubatko, Laura Salter 3 Long, Colby 3 Molloy, Erin K. 3 Rhodes, John Anthony 3 Roch, Sébastien 2 Allman, Elizabeth S. 2 Bayzid, Md. Shamsuzzoha 2 Christensen, Sarah 2 Hill, Max 2 Legried, Brandon 2 Mirarab, Siavash 2 Richards, Andrew 2 Vachaspati, Pranjal 1 Balaban, Metin 1 Bell, Rayna 1 Biswas, Avijit 1 Degnan, James H. 1 Desper, Richard 1 Gascuel, Olivier 1 Grindstaff, Gillian Roxanne 1 Gross, Elizabeth 1 Jiang, Yueyu 1 Kane, Daniel M. 1 Lafond, Manuel 1 Mahbub, Sazan 1 Navid, Bin Hasan 1 Owen, Megan 1 Pouryahya, Fatemeh 1 Rahman, Mohammad Sohel 1 Reaz, Rezwana 1 Rusinko, Joseph 1 Saha, Arpita 1 Sankoff, David 1 Sawmya, Shashata 1 Scornavacca, Celine 1 Tabaghi, Puoya 1 Tao, Terence 1 Willis, Amy D. 1 Yourdkhani, Samaneh all top 5 Cited in 8 Serials 4 Bulletin of Mathematical Biology 2 Journal of Theoretical Biology 2 SIAM Journal on Applied Algebra and Geometry 1 Theoretical Computer Science 1 The Annals of Applied Probability 1 The Electronic Journal of Combinatorics 1 Computational Biology 1 Journal of Computational and Graphical Statistics all top 5 Cited in 9 Fields 20 Biology and other natural sciences (92-XX) 3 Combinatorics (05-XX) 3 Computer science (68-XX) 2 Statistics (62-XX) 1 General and overarching topics; collections (00-XX) 1 Number theory (11-XX) 1 Convex and discrete geometry (52-XX) 1 Probability theory and stochastic processes (60-XX) 1 Operations research, mathematical programming (90-XX) Citations by Year