IQ-TREE 3: phylogenomic inference software using complex evolutionary models

By T. K. Wong, Nhan Ly-Trong, Huaiyan Ren, Piyumal Demotte, H. Baños, Andrew J. Roger, E. Susko, Chris Bielow, N. de Maio, Nick Goldman and 6 more. Molecular biology and evolution, 2026

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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.

Subfields: Artificial Intelligence, Genetics

View Paper: https://www.semanticscholar.org/paper/448d3eb4bc1e2da7bf403eaf98df070ae5e1a2f5