Molecular Biology and Evolution· 2026Q1
IQ-TREE 3: phylogenomic inference software using complex evolutionary models
- 423citations
- Q1SCImago
- 2026year
Short summary
IQ-TREE 3, a major update to the popular phylogenetics software, now infers evolutionary trees using mixture models and quantifies discordance between genomic regions with gene and site concordance factors.
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Key points
- IQ-TREE 3 offers mixture models as an alternative to partitioned models for phylogenetic inference.
- New gene and site concordance factors quantify discordance between genomic regions.
- The software now integrates with phylogenomic divergence time estimation.
- A fully featured sequence simulator is included in IQ-TREE 3.
AI-generated from the title and abstract; the full text is not read.
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.
The authors' abstract, as published at the source. Molecular Biology and Evolution, 2026 · DOI ↗
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Field: Genetics (Biochemistry, Genetics and Molecular Biology) Molecular Biology
Molecular BiologyBiochemistry, Genetics and Molecular BiologyGenetics