Phylo2Vec

Phylo2Vec is a high-performance software package for encoding, manipulating, and analyzing binary phylogenetic trees. At its core, the package contains representation of binary trees, which defines a bijection from any tree topology with 𝑛 leaves into an integer vector of size 𝑛 − 1. Compared to the traditional Newick format, phylo2vec was designed with fast sampling and rapid tree comparison in mind.

This current 2.0 version features a core implementation in Rust, providing significant performance improvements and memory efficiency while remaining available in Python (superseding the version described in the original paper (Penn et al., 2024)) and R via dedicated wrappers, making it accessible to a broad audience in the bioinformatics community.

Link to the paper: https://doi.org/10.1093/sysbio/syae030

Installation

Dependencies

• python>=3.10
• numba>=0.56.4
• numpy>=1.22,<2.1
• biopython>=1.84.0
• joblib>=1.2.0
• ete3==3.1.3
• six>=1.16.0

User installation

Pip

The easiest way to install the Python package is using pip:

pip install phylo2vec

Manual installation

• We recommend setting up pixi package management tool.
• Clone the repository and install using pixi:

git clone https://github.com/sbhattlab/phylo2vec.git
cd phylo2vec
pixi run -e py-phylo2vec install-python

This will compile and install the package as the core functionality is written in Rust.

Installing R package

To install the R package, first you need to retrieve one of the compiled file within the package releases. Once the file is downloaded, simply run install.packages in your R command line.

install.packages("/path/to/package_file", repos = NULL, type = 'source')

Basic Usage

Python

Conversion between Newick and vector representations

import numpy as np
from phylo2vec.base import to_newick, to_vector

# Convert a vector to Newick string
v = np.array([0, 1, 2, 3, 4])
newick = to_newick(v)  # '(0,(1,(2,(3,(4,5)6)7)8)9)10;'

# Convert Newick string back to vector
v_converted = to_vector(newick)  # array([0, 1, 2, 3, 4], dtype=int16)

Tree Manipulation

from phylo2vec.utils import add_leaf, remove_leaf, reroot_at_random

# Add a leaf to an existing tree
v_new = add_leaf(v, 2)  # Add a leaf to the third position

# Remove a leaf
v_reduced = remove_leaf(v, 1)  # Remove the second leaf

# Random rerooting
v_rerooted = reroot_at_random(v)

Optimization

from phylo2vec.opt import HillClimbingOptimizer

# Perform phylogenetic inference
hc = HillClimbingOptimizer(raxml_cmd="/path/to/raxml-ng", verbose=True)
v_opt, taxa_dict, losses = hc.fit("/path/to/your_fasta_file.fa")

Documentation

For comprehensive documentation, tutorials, and API reference, visit: https://phylo2vec.readthedocs.io

How to Contribute

We welcome contributions to Phylo2Vec! Here's how you can help:

1. Fork the repository and create your branch from main
2. Make your changes and add tests if applicable
3. Run the tests to ensure they pass
4. Submit a pull request with a detailed description of your changes

Please make sure to follow our coding standards and write appropriate tests for new features.

Thanks to our contributors so far!

License

This project is distributed under the GNU Lesser General Public License v3.0 (LGPL).

Citation

If you use Phylo2Vec in your research, please cite:

@article{10.1093/sysbio/syae030,
    author = {Penn, Matthew J and Scheidwasser, Neil and Khurana, Mark P and Duchêne, David A and Donnelly, Christl A and Bhatt, Samir},
    title = {Phylo2Vec: a vector representation for binary trees},
    journal = {Systematic Biology},
    year = {2024},
    month = {03},
    doi = {10.1093/sysbio/syae030},
    url = {https://doi.org/10.1093/sysbio/syae030},
}

Related Work

• Preprint repository (core functions are deprecated): https://github.com/Neclow/phylo2vec_preprint
• C++ version (deprecated): https://github.com/Neclow/phylo2vec_cpp
• GradME: https://github.com/Neclow/GradME = phylo2vec + minimum evolution + gradient descent