IQ-TREE 3: phylogenomic inference software using complex evolutionary models
2026/05/01 by Thomas K. F. Wong, Thomas K F Wong, Nhan Ly-Trong +17 · 3 voices · 376 citations
Biochemistry, Genetics and Molecular Biology · Computer Science · Mathematics · #Artificial intelligence #Biology #Clade #Computer science #Evolution and Genetic Dynamics #Evolutionary Algorithms and Applications #Genetics #Inference #Machine learning #Mathematics #Phylogenetics #Phylogenomics #Programming language #Software #Software development #Software evolution #Tree (set theory)
paper · doi:10.1093/molbev/msag117
published in Molecular Biology and Evolution 43(5) (Oxford University Press)
openalex created_date 2025/10/10 · openalex publication_date 2026/05/01 · openalex updated_date 2026/08/06
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.
Citations
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Discussions
- Wong et al. present IQ-TREE version 3, with new features including mixture models, gene and site concordance factors, integration with phylogenomic divergence time estimation, and a fully featured seq [bsky, 56 points, 1 comments]
- Wong et al. (2026-05, Molecular Biology and Evolution)（オープンアクセス open access） 「IQ-TREE 3：複雑な進化モデルを用いたゲノム系統推論ソフトウェア」 IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models doi.org/ [bsky, 3 points, 0 comments]
- IQ-TREE3はMBEから出たんですね。 doi.org/10.1093/molb... [bsky, 2 points, 0 comments]
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