IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models

Thomas K.F. Wong, Nhan Ly-Trong, Huaiyan Ren, Hector Baños, Andrew J. Roger, Edward Susko, Chris Bielow, Nicola De Maio, Nick Goldman, Matthew W Hahn, Gavin Huttley, Rob Lanfear, Bui Quang Minh

IQ-TREE (http://www.iqtree.org) 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, and a fully-featured sequence simulator. The IQ-TREE 3 source code is available at https://github.com/iqtree/iqtree3.