piqtree

piqtree exposes IQ-TREE's phylogenetic inference engine through Python functions for phylogenetic reconstruction, ultrafast bootstrapping, branch length optimisation, ModelFinder, and rapid neighbour-joining, enabling interoperability with Python libraries via the cogent3 package.

Key Features:

• Phylogenetic reconstruction: Performs phylogenetic tree inference using IQ-TREE's algorithms.
• Ultrafast bootstrapping: Provides access to IQ-TREE's ultrafast bootstrap approximation for branch support.
• Branch length optimisation: Enables optimisation of branch lengths on phylogenetic trees.
• ModelFinder: Supports automated selection of best-fit substitution models for phylogenetic analysis.
• Rapid neighbour-joining: Implements fast neighbour-joining tree construction.
• Python interoperability: Integrates with other Python libraries and tools through the cogent3 package.

Scientific Applications:

• Phylogenetic workflow development: Simplifies construction of phylogenetic analysis pipelines by exposing IQ-TREE capabilities within Python environments.
• Interactive phylogenetic analysis: Enables interactive phylogenetic computations in Jupyter notebooks and other Python-based interactive environments.

Methodology:

piqtree directly exposes IQ-TREE's phylogenetic inference engine through Python functions, with interoperability mediated by the cogent3 package.