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Updated: May 7, 2026

A Practical Guide to Phylogenetics for Nonexperts
Published on: February 5, 2014
IQ-TREE 3: phylogenomic inference software using complex evolutionary models
Thomas K F Wong1,2, Nhan Ly-Trong1, Huaiyan Ren1
1School of Computing, College of Systems and Society, Australian National University, Canberra, ACT, Australia.
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.
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