IQ-TREE 3: phylogenomic inference software using complex evolutionary models

作者：Thomas K. F. Wong, Nhan Ly-Trong, Huaiyan Ren, Piyumal Demotte, Hector Baños, Andrew J. Roger, Edward Susko, Chris Bielow, Nicola De Maio, Nick Goldman, Matthew W. Hahn, Mario dos Reis, Bùi Quang Minh, Gavin Huttley, Robert Lanfear, Bùi Quang Minh · 发表于：Molecular Biology and Evolution · 年份：2026 · DOI：10.1093/molbev/msag117 · 被引用次数：378 · 研究领域：Evolution and Genetic Dynamics、Evolutionary Algorithms and Applications

IQ-TREE (https://iqtree.github.io/) is a widely used open-source software tool for efficiently inferring phylogenetic trees under maximum likelihood. Here, we present IQ-TREE version 3, the third major release of the software. IQ-TREE 3 significantly extends version 2 with new features, including mixture models as an alternative to partitioned models, gene and site concordance factors to quantify discordance between genomic regions, integration with phylogenomic divergence time estimation, and a fully featured sequence simulator. The IQ-TREE 3 source code is available at https://github.com/iqtree/iqtree3.