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

<monospace>piqtree</monospace> 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, <monospace>piqtree</monospace> greatly simplifies the development of new phylogenetic workflows through seamless interoperability with other Python libraries and tools mediated by the <monospace>cogent3</monospace> 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 <monospace>piqtree</monospace> library and a small case study that showcases its interoperability. The <monospace>piqtree</monospace> library can be installed with <monospace>pip install piqtree</monospace>, with the documentation available at <ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="https://piqtree.readthedocs.io">https://piqtree.readthedocs.io</ext-link> and source at <ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="https://github.com/iqtree/piqtree">https://github.com/iqtree/piqtree</ext-link>.