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},
}