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bioRxiv · 10.1101/2025.07.13.664626

piqtree: A Python Package for Seamless Phylogenetic Inference with IQ-TREE

McArthur, R. N.·Wong, T. K. F. N.·Lang, Y.·Morris, R. A.·Caley, K.·Mallawaarachchi, V.·Minh, B. Q.·Huttley, G. A.
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Abstract

piqtree (pronounced pie-cue-tree) is an easy to use, open-source Python package that provides Python script based control of IQ-TREEs phylogenetic inference engine. piqtree builds IQ-TREE as a Python package, presenting a library of Python functions for performing many of IQ-TREEs capabilities including phylogenetic reconstruction, ultrafast bootstrapping, branch length optimization, model selection, rapid neighbor-joining, alignment simulation, and more. As piqtree explicitly uses IQ-TREEs phylogenetic algorithms, the computational and statistical performance of piqtree equal that of IQ-TREE. Modestly higher memory usage may be expected owing to the Python runtime and the need to load the alignment in Python. By exposing IQ-TREEs algorithms within Python, piqtree offers users a greatly simplified experience in development of phylogenetic workflows through seamless interoperability with other Python libraries and tools mediated by the cogent3 package. It enables users to perform interactive phylogenetic analyses and visualization using, for instance, Jupyter notebooks. We present the key features available in the piqtree library and a small case study that showcases its interoperability. piqtree is distributed for use as a standard Python package at https://pypi.org/project/piqtree/, documentation is available at https://piqtree.readthedocs.io and source code at https://github.com/iqtree/piqtree.

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McArthur, R. N., Wong, T. K. F. N., Lang, Y., Morris, R. A., Caley, K., Mallawaarachchi, V., Minh, B. Q., Huttley, G. A.. 2025-07-16. piqtree: A Python Package for Seamless Phylogenetic Inference with IQ-TREE. https://doi.org/10.1101/2025.07.13.664626

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