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

K. F. Wong, Thomas; Ly-Trong, Nhan; Ren, Huaiyan; Demotte, Piyumal; Baños, Hector; J. Roger, Andrew; Susko, Edward; Bielow, Chris; De Maio, Nicola; Goldman, Nick; W. Hahn, Matthew; dos Reis, Mario; Quang Minh, Bùi; Huttley, Gavin; Lanfear, Robert; Quang Minh, Bùi

doi:10.1093/molbev/msag117

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

Published in Molecular Biology and Evolution • May 1, 2026

Authors:

Thomas K. F. Wong

Nhan Ly-Trong

Huaiyan Ren

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 mi...

Subject

Inference

Computer science

Tree (set theory)

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