Preprint

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

Thomas K. F. WongAustralian National UniversityNhan Ly-TrongAustralian National UniversityHuaiyan RenAustralian National UniversityHector BañosAustralian National UniversityAndrew J. RogerDalhousie UniversityEdward SuskoDalhousie UniversityChris BielowDalhousie UniversityNicola De MaioFreie Universität BerlinNick GoldmanEuropean Bioinformatics InstituteMatthew W. HahnEuropean Bioinformatics InstituteGavin HuttleyIndiana University BloomingtonRobert LanfearQueen Mary University of LondonBùi Quang MinhVietnam National University, Hanoi

2025en

ABI

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.

Identifiers

DOI: 10.1093/molbev/msag117

Citations and references

Cited by 20 references

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