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piqtree is an easy to use, open-source Python package that directly exposes IQ-TREE’s phylogenetic inference engine. It offers Python functions for performing many of IQ-TREE’s capabilities including phylogenetic reconstruction, ultrafast bootstrapping, branch length optimisation, ModelFinder, rapid neighbour-joining, and more. By exposing IQ-TREE’s algorithms within Python, piqtree greatly simplifies the development of new phylogenetic workflows through seamless interoperability with other Python libraries and tools mediated by the cogent3 package. It also enables users to perform interactive analyses with IQ-TREE through, for instance, Jupyter notebooks. We present the key features available in the piqtree library and a small case study that showcases its interoperability. The piqtree library can be installed withpip install piqtree, with the documentation available at https://piqtree.readthedocs.io and source at https://github.com/iqtree/piqtree.
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This content will become publicly available on April 7, 2026
IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models
IQ-TREE (http://www.iqtree.org) 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, and a fully-featured sequence simulator. The IQ-TREE 3 source code is available at https://github.com/iqtree/iqtree3.
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- Award ID(s):
- 2333243
- PAR ID:
- 10621346
- Publisher / Repository:
- ecoevorxiv
- Date Published:
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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