piqtree: a python package for seamless phylogenetic inference with IQ-TREE

Area of Science:

• Computational Biology
• Bioinformatics
• Phylogenetics

Background:

• Phylogenetic inference is crucial for understanding evolutionary relationships.
• IQ-TREE is a high-performance engine for phylogenetic analysis.
• Integrating complex bioinformatics tools into user-friendly workflows remains a challenge.

Purpose of the Study:

• To introduce piqtree, an open-source Python package for controlling IQ-TREE.
• To simplify the development of phylogenetic workflows through Python scripting.
• To enhance interoperability between phylogenetic inference and other Python tools.

Main Methods:

• piqtree wraps IQ-TREE's core algorithms as Python functions.
• Leverages the cogent3 package for seamless integration with the Python ecosystem.
• Provides functionalities for phylogenetic reconstruction, bootstrapping, model selection, and more.

Main Results:

• piqtree offers computational and statistical performance equivalent to IQ-TREE.
• Enables interactive phylogenetic analyses and visualization, e.g., in Jupyter notebooks.
• Demonstrates simplified development of phylogenetic workflows via a case study.

Conclusions:

• piqtree successfully bridges IQ-TREE's high-performance inference with user-friendly Python interfaces.
• Facilitates easier development and execution of complex phylogenetic analyses.
• Enhances accessibility and integration of advanced phylogenetic tools for researchers.