Install iqtree3 with Homebrew, MacPorts

Project links

• Homepage
• Repository
• Upstream docs
• Package manager page

Commands and aliases

• iqtree3

Project history

The IQ-TREE README says the software was created as the successor of IQPNNI and TREE-PUZZLE, which explains the name. It was motivated by the growth of phylogenomic data and the need for efficient software that could handle larger alignments and more complex models of sequence evolution.

The first widely cited IQ-TREE paper appeared in 2015, presenting a fast stochastic algorithm for estimating maximum-likelihood phylogenies. The README also points to the 2020 IQ-TREE 2 paper for new models and efficient methods in the genomic era, and the 2026 IQ-TREE 3 citation for complex evolutionary models.

IQ-TREE 3 continues the line in a separate GitHub repository while preserving lineage to IQ-TREE 1 and IQ-TREE 2 releases. Its README highlights features such as ModelFinder, ultrafast bootstrap, partition and mixture models, AliSim, topology tests, checkpointing, multicore execution, and distributed parallel computing.

Adoption history

IQ-TREE was adopted in computational biology because it combined speed, model breadth, and practical command-line ergonomics. Its feature papers for UFBoot, ModelFinder, W-IQ-TREE, IQ-TREE 2, and IQ-TREE 3 document a path from standalone tree search to a broad phylogenomic platform.

The README advertises GitHub release downloads, BioConda installs, web-server access, and package-manager distribution. Homebrew's iqtree3 formula gives macOS command-line users a versioned package for the third major generation.

How it is used

Users run iqtree3 on sequence alignments in formats such as PHYLIP, FASTA, Nexus, Clustal, and MSF. Outputs include an .iqtree report and a Newick .treefile that can be viewed in tree visualization tools.

Common workflows include maximum-likelihood tree inference, automatic substitution-model selection, ultrafast bootstrap support analysis, partitioned analyses, mixture models, topology tests, polymorphism-aware models, and alignment simulation.

Why package nerds care

IQ-TREE 3 is package-nerd significant because scientific command-line packaging has to preserve exact executable names, citations, bundled model support, OpenMP/MPI-style performance expectations, and reproducible outputs. A package upgrade is not just a binary refresh; it can affect published methods and citation guidance.

It also illustrates the biology-tool pattern where the README is part manual, part citation map, and part dependency history, linking features to papers and predecessor projects.

Timeline

• 2013: UFBoot is published as an ultrafast bootstrap approximation associated with IQ-TREE workflows.
• 2015: IQ-TREE version 1 paper presents fast maximum-likelihood phylogeny estimation.
• 2016: W-IQ-TREE web server paper documents online IQ-TREE access.
• 2017: ModelFinder paper documents fast model selection used by IQ-TREE.
• 2020: IQ-TREE 2 paper presents new models and efficient genomic-era methods.
• 2023: AliSim-HPC paper documents parallel sequence simulation support.
• 2026: IQ-TREE 3 citation describes phylogenomic inference software using complex evolutionary models.

Related projects

• IQ-TREE 3 relates to IQPNNI, TREE-PUZZLE, IQ-TREE 1, IQ-TREE 2, RAxML, PhyML, ModelFinder, UFBoot, AliSim, W-IQ-TREE, BioConda, CIPRES, FigTree, Dendroscope, and iTOL.

Sources

• https://formulae.brew.sh/formula/iqtree3
• https://github.com/iqtree/iqtree3
• https://raw.githubusercontent.com/iqtree/iqtree3/master/README.md
• https://www.iqtree.org/doc
• https://www.iqtree.org/doc/iqtree-doc.pdf