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Title: piqtree: A Python Package for Seamless Phylogenetic Inference with IQ-TREE
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.  more » « less
Award ID(s):
2333243
PAR ID:
10621351
Author(s) / Creator(s):
; ; ; ; ; ; ;
Publisher / Repository:
bioRxiv
Date Published:
Format(s):
Medium: X
Institution:
bioRxiv
Sponsoring Org:
National Science Foundation
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