title: IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies.
abstract: Large phylogenomics data sets require fast tree inference methods, especially for maximum-likelihood (ML) phylogenies. Fast programs exist, but due to inherent heuristics to find optimal trees, it is not clear whether the best tree is found. Thus, there is need for additional approaches that employ different search strategies to find ML trees and that are at the same time as fast as currently available ML programs. We show that a combination of hill-climbing approaches and a stochastic perturbation method can be time-efficiently implemented. If we allow the same CPU time as RAxML and PhyML, then our software IQ-TREE found higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring the tree-space. If we use the IQ-TREE stopping rule, RAxML and PhyML are faster in 75.7% and 47.1% of the DNA alignments and 42.2% and 100% of the protein alignments, respectively. However, the range of obtaining higher likelihoods with IQ-TREE improves to 73.3-97.1%. IQ-TREE is freely available at http://www.cibiv.at/software/iqtree.
authors.affiliation: Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, Vienna, Austria Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria.
authors.forename: Lam-Tung
authors.initials: LT
authors.lastname: Nguyen
authors.affiliation: Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, Vienna, Austria.
authors.forename: Heiko A
authors.initials: HA
authors.lastname: Schmidt
authors.affiliation: Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, Vienna, Austria Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria.
authors.forename: Arndt
authors.initials: A
authors.lastname: von Haeseler
authors.affiliation: Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, Vienna, Austria minh.bui@univie.ac.at.
authors.forename: Bui Quang
authors.initials: BQ
authors.lastname: Minh
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D016678:Genome; D016013:Likelihood Functions; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D012984:Software; D013997:Time Factors
keywords: maximum likelihood; phylogenetic inference; phylogeny; stochastic algorithm