piqtree: IQ-TREE2 meets Python via cogent3

[GavinHuttley]

The developers of IQ-TREE2 and cogent3 have joined forces to bring the power of IQ-TREE2 to Python users as piqtree.

piqtree exposes selected IQ-TREE2 capabilities within Python, using the cogent3 library as the interface. piqtree is an addition to, not a replacement of, IQ-TREE2.

The piqtree project has the goals of:

• making the individual high-performance components of IQ-TREE2 available within Python, enabling the community to take advantage of these routines
• enable exploratory analyses in interactive Jupyter notebooks

You are now just a pip install piqtree away from trying it out!

piqtree capabilities

piqtree provides standard Python functions for performing key analyses, e.g. model finder, phylogenetic estimation with bootstrapping and more! It also 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.

You can find the piqtree documentation here and the source code repository with bug tracker and forum.

Note

piqtree is NOT a full replacement of IQ-TREE2. Users who want the full power of IQ-TREE2 can still use the command line application.

An invitation to the community

piqtree does not yet implement all of the capabilities of IQ-TREE2 but is under active development. If there are features you want, go to the forum and tell us, or vote on other proposals.

And if you like the piqtree and cogent3 projects, give us a GitHub ⭐!

A call to action

You don't have to be a developer to participate in these projects! For example, we really need assistance from a Windows based Python developer with experience with compiled extensions (see this issue).

To get started, check out the piqtree issues and cogent3 issues pages and select something you'd like to work on. Filter them on "good first issue" as a starting point.