piqtree
piqtree (pronounced 'pie-cue-tree') is a library which allows you to use IQ-TREE directly from Python! The interface with Python is through cogent3 objects.
For usage, please refer to the documentation or the examples below.
If you encounter any problems or have any feature requests feel free to raise an issue!
Contributing
If you would like to help out by contributing to the piqtree project, please check out our contributor guide!
Examples
Phylogenetic Reconstruction
from piqtree import build_tree
from cogent3 import load_aligned_seqs # Included with piqtree!
# Load Sequences
aln = load_aligned_seqs("tests/data/example.fasta", moltype="dna")
aln = aln.take_seqs(["Human", "Chimpanzee", "Rhesus", "Mouse"])
# Reconstruct a phylogenetic tree with IQ-TREE!
tree = build_tree(aln, "JC", rand_seed=1) # Optionally specify a random seed.
print("Tree topology:", tree) # A cogent3 tree object
print("Log-likelihood:", tree.params["lnL"])
# In a Jupyter notebook, try tree.get_figure() to see a dendrogram
Note See the cogent3 docs for examples on what you can do with cogent3 trees.
Fit Branch Lengths to Tree Topology
from piqtree import fit_tree
from cogent3 import load_aligned_seqs, make_tree
# Load Sequences
aln = load_aligned_seqs("tests/data/example.fasta", moltype="dna")
aln = aln.take_seqs(["Human", "Chimpanzee", "Rhesus", "Mouse"])
# Construct tree topology
tree = make_tree("(Human, Chimpanzee, (Rhesus, Mouse));")
# Fit branch lengths with IQ-TREE!
tree = fit_tree(aln, tree, "JC")
print("Tree with branch lengths:", tree)
print("Log-likelihood:", tree.params["lnL"])
More
For more examples ranging from using ModelFinder and AliSim, to making rapid neighbour-joining trees, or randomly generated trees be sure to check out the documentation!
Citation
Please cite
@article{10.1093/molbev/msag061,
author = {McArthur, Robert Neil and Wong, Thomas King-Fung and Lang, Yapeng and Morris, Richard Andrew and Caley, Katherine and Mallawaarachchi, Vijini and Minh, Bui Quang and Huttley, Gavin},
title = {piqtree: A Python Package for Seamless Phylogenetic Inference with IQ-TREE},
journal = {Molecular Biology and Evolution},
year = {2026},
pages = {msag061},
doi = {10.1093/molbev/msag061},
url = {https://doi.org/10.1093/molbev/msag061},
}
1 maintainer
Release files for piqtree 0.8.3
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Built distributions (wheels)
| File | Reset | |||
|---|---|---|---|---|
| piqtree-0.8.3-cp314-cp314-win_amd64.whl | CPython 3.14 | CPython 3.14 | Windows x86-64 | Details |
| piqtree-0.8.3-cp314-cp314-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl | CPython 3.14 | CPython 3.14 | Linux glibc 2.28+ x86-64, Linux glibc 2.24+ x86-64 | Details |
| piqtree-0.8.3-cp314-cp314-macosx_15_0_arm64.whl | CPython 3.14 | CPython 3.14 | macOS 15.0+ ARM64 | Details |
| piqtree-0.8.3-cp313-cp313-win_amd64.whl | CPython 3.13 | CPython 3.13 | Windows x86-64 | Details |
| piqtree-0.8.3-cp313-cp313-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl | CPython 3.13 | CPython 3.13 | Linux glibc 2.24+ x86-64, Linux glibc 2.28+ x86-64 | Details |
| piqtree-0.8.3-cp313-cp313-macosx_15_0_arm64.whl | CPython 3.13 | CPython 3.13 | macOS 15.0+ ARM64 | Details |
| piqtree-0.8.3-cp312-cp312-win_amd64.whl | CPython 3.12 | CPython 3.12 | Windows x86-64 | Details |
| piqtree-0.8.3-cp312-cp312-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl | CPython 3.12 | CPython 3.12 | Linux glibc 2.28+ x86-64, Linux glibc 2.24+ x86-64 | Details |
| piqtree-0.8.3-cp312-cp312-macosx_15_0_arm64.whl | CPython 3.12 | CPython 3.12 | macOS 15.0+ ARM64 | Details |
Total release size: 66.9 MB
Release files / piqtree-0.8.3-cp314-cp314-win_amd64.whl
| Download URL | piqtree-0.8.3-cp314-cp314-win_amd64.whl |
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| Size | 14.0 MB |
| Tags | CPython 3.14 Windows x86-64 |
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