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piqtree documentation

Overview

piqtree is a Python package that exposes selected IQ-TREE 2 capabilities within Python, using the cogent3 library as the interface.

piqtree is implemented with the goals of:

  • making the individual high-performance components of IQ-TREE 2 available within Python, enabling the community to take advantage of these routines.
  • facilitating exploratory analyses by leveraging cogent3's capabilities to provide a rich user experience in interactive Jupyter notebooks, e.g. trivial parallelisation across collections of alignments.
  • code using piqtree apps should be easy to understand.

In addition to the functions provided, piqtree provides mini-applications in the form of cogent3 apps. These can interplay with other such apps, e.g. the cogent3-ete3 tree conversion plugin, the diverse-seqs sequence subsampling plugin.

Note piqtree does not implement all of the capabilities of IQ-TREE 2!

Installation

You get the vanilla version of piqtree by running the following command.

pip install piqtree

To get visualisation support with plotly, use the [extra] option.

pip install "piqtree[extra]"

Supported platforms

At present we do not provide native binaries for Windows. Windows users can run piqtree using the Windows Subsystem for Linux (WSL) which can installed via the Windows Store.