# IQ-TREE

> software

**Wikidata**: [Q113018370](https://www.wikidata.org/wiki/Q113018370)  
**Source**: https://4ort.xyz/entity/iq-tree

## Summary
IQ-TREE is a software tool designed for phylogenetic inference, enabling researchers to construct evolutionary trees using maximum-likelihood methods. It is specifically developed to handle the computational challenges of analyzing large genomic datasets efficiently.

## Key Facts
- **Classification**: IQ-TREE is an instance of software (a non-tangible executable component of a computer).
- **Funding**: Received a grant from the Chan Zuckerberg Initiative under the Essential Open Source Software for Science program (as of September 6, 2022).
- **Current Stable Version**: 3.0.1 (released May 5, 2025).
- **Website**: http://www.iqtree.org/ (primarily in English).
- **Source Code Repository**: Available at https://github.com/iqtree/iqtree3 (hosted on GitHub, a free and open source software repository).
- **Described By**: Key sources include "IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies" and "IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era".
- **Package Availability**: Available via MacPorts (iqtree) and SlackBuilds (academic/iqtree).

## FAQs
### Q: What is IQ-TREE used for?
A: IQ-TREE is software used for phylogenetic inference, primarily for constructing evolutionary trees (phylogenies) from sequence data using maximum-likelihood methods.

### Q: Who funds IQ-TREE development?
A: IQ-TREE received grant funding from the Chan Zuckerberg Initiative through its Essential Open Source Software for Science program, confirmed as of September 6, 2022.

### Q: Where can I download IQ-TREE or its source code?
A: The official website is http://www.iqtree.org/. The source code is available on GitHub at https://github.com/iqtree/iqtree3. It can also be installed via package managers like MacPorts and SlackBuilds.

## Why It Matters
IQ-TREE addresses a critical challenge in evolutionary biology: the efficient analysis of increasingly large and complex genomic datasets. By providing fast and effective stochastic algorithms for maximum-likelihood phylogenetic inference, it enables researchers to reconstruct evolutionary histories with greater accuracy and speed than many predecessors. This capability is essential for understanding biodiversity, disease evolution, and fundamental biological processes at the genomic scale. Its development and support under programs like the Essential Open Source Software for Science initiative underscore its importance as a foundational tool in modern computational phylogenetics.

## Notable For
- Being specifically cited as "Essential Open Source Software for Science" by the Chan Zuckerberg Initiative (2022).
- The release of version 2.0 introducing new models and efficient methods for phylogenetic inference in the genomic era.
- Providing a dedicated, optimized maximum-likelihood inference algorithm for large phylogenomic analyses.
- Its continuous development and active maintenance on platforms like GitHub.

## Body
### Funding & Development
- Funding for IQ-TREE includes a grant from the Chan Zuckerberg Initiative awarded under the Essential Open Source Science (EOSS) program (reference date: 2022-09-06; source: Chan Zuckerberg Initiative EOSS proposals).
- The software is actively maintained, with source code hosted on GitHub (https://github.com/iqtree/iqtree3).

### Version Information
- The current stable version is 3.0.1 (released May 5, 2025).
- Version 3.0.1 is explicitly marked as the stable version (as of reference date: 2025-11-15; source: GitHub release tag v3.0.1).
- Significant evolution occurred with IQ-TREE 2.0, which introduced new models and efficient methods tailored for phylogenetic inference in the genomic era.

### Distribution & Accessibility
- The official website is http://www.iqtree.org/ (primarily in English).
- The software can be installed via package management systems:
    - MacPorts: `iqtree`
    - SlackBuilds: `academic/iqtree`
- IQ-TREE is classified as software (non-tangible executable component).

### Academic Foundation
- The software is described by key academic sources:
    - "IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies"
    - "IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era"

## References

1. [Release 3.0.1. 2025](https://github.com/iqtree/iqtree3/releases/tag/v3.0.1)
2. [Release 3.1.0. 2026](https://github.com/iqtree/iqtree3/releases/tag/v3.1.0)
3. [Release 3.1.1. 2026](https://github.com/iqtree/iqtree3/releases/tag/v3.1.1)
4. [Source](https://chanzuckerberg.com/eoss/proposals/)