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

Molecular Biology and Evolution 2026 Open access

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Authors: 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
+4 more Bùi Quang Minh, Gavin Huttley, Robert Lanfear, Bùi Quang Minh
DOI: 10.1093/molbev/msag117
Cited by: 394
References: 75

Abstract

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.

Fields of Study & Subjects

Evolution and Genetic Dynamics Evolutionary Algorithms and Applications

Publication details

Journal / source
Molecular Biology and Evolution
Publisher
Oxford University Press (OUP)
Volume
43
Issue
5
Publication date
1 May 2026
Language
EN