Introduction

Overview

piqtree (pronounced 'pie-cue-tree') is a Python package that exposes selected IQ-TREE 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 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!

Installation

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

pip install piqtree

To get Jupyter and visualisation support (with plotly) use the [extra] option.

pip install "piqtree[extra]"

Sharing your cool solutions 😎

If you've done something you would like to share which either used piqtree or helped you to it (e.g. some data sampling steps with cogent3), please share your code on our community contribution site. Contributing is as easy as clicking a button and pasting your code! Who knows, it may lead to collaborations 🙂.

If you want to see how others are using piqtree, take a look at the site. (At the time of writing, this is very new, so there's not many contributions.)

Getting help

If you have a question about using piqtree, you can post a question in the piqtree forums. Likewise, if you have any questions about using cogent3, post a question in the cogent3 forums.

Reporting problems

To report problems or potential bugs 🐛, please raise an issue on the piqtree GitHub issues page.

Citing piqtree

Please cite our preprint.