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A Practical Guide to Phylogenetics for Nonexperts
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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.
Molecular Biology and Evolution
|May 5, 2026
Summary
IQ-TREE version 3 is a new release of phylogenetic tree inference software. This update introduces mixture models, concordance factors for genomic discordance, and divergence time estimation integration.
Area of Science:
- Computational Biology
- Phylogenetics
- Bioinformatics
Background:
- IQ-TREE is a popular open-source tool for phylogenetic tree inference using maximum likelihood.
- The previous version, IQ-TREE 2, established a robust foundation for evolutionary analyses.
Purpose of the Study:
- To introduce IQ-TREE version 3, the latest major release of the phylogenetic inference software.
- To highlight significant new features and improvements over IQ-TREE version 2.
Main Methods:
- Development and implementation of new algorithms within the IQ-TREE software framework.
- Integration of novel statistical methods for phylogenetic analysis.
Main Results:
- IQ-TREE 3 incorporates mixture models as an alternative to partitioned models.
- New features include gene and site concordance factors to assess genomic region discordance.
- Integration with phylogenomic divergence time estimation and a sequence simulator are now available.
Conclusions:
- IQ-TREE 3 offers enhanced capabilities for phylogenetic tree inference and evolutionary analysis.
- The new features provide more accurate and comprehensive insights into evolutionary relationships and genomic discordance.
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