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

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.

• NS
  National Science Foundation

  Awards: DMS-2331660, 2331660, DBI-2146866, 2146866
• GA
  Gordon and Betty Moore Foundation

  Award: 735923LPI
• NF
  National Foundation for Science and Technology Development

  Award: 102.05-2025.65
• NC
  National Computational Infrastructure
• EM
  European Molecular Biology Laboratory
• CZ
  Chan Zuckerberg Initiative

  Awards: EOSS4-0000000312, EOSS-0000000132, EOSS5-0000000223
• AG
  Australian Government
• EA
  EMBL Australia

  Award: MR/Z503526/1
• NI
  National Institute for Health and Care Research
• NS
  Natural Sciences and Engineering Research Council of Canada
• MR
  Medical Research Council

  Award: MR/Z503526/1
• BA
  Biotechnology and Biological Sciences Research Council

  Award: BB/T01282X/1
• NC
  National Cancer Institute
• CO
  Centre of Excellence for Quantum Computation and Communication Technology, Australian Research Council

  Award: DP200103151
• CF
  Centre for Innovation in Biomedical Imaging Technology, Australian Research Council

  Award: IC210100047