phylo2vec 0.1.9

Phylo2Vec: integer vector representation of binary (phylogenetic) trees

Phylo2Vec

This repository contains an implementation of Phylo2Vec. It is distributed under the GNU Lesser General Public License v3.0 (LGPL).

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

Installation

Dependencies

• python>=3.9
• numba==0.56.4
• numpy==1.23.5
• biopython==1.80.0
• joblib>=1.2.0
• ete3==3.1.3

User installation

Pip

pip install phylo2vec

Manual installation

• We recommend to setup an isolated enviroment, using conda, mamba or virtualenv.
• Clone the repository and install using pip:

git clone https://github.com/Neclow/phylo2vec_dev.git
pip install -e .

Development

Additional test dependencies

• pytest==7.4.2
• six==1.16.0

Testing

After installation, you can launch the test suite from outside the source directory:

pytest phylo2vec

Warning! You might need to clear your __pycache__ folders beforehand:

rm -rf phylo2vec/__pycache__/
rm -rf phylo2vec/base/__pycache__/

Basic usage

Conversions

• The base module contains elements to convert a Newick string (to_vector) to a Phylo2Vec vector and vice versa (to_newick)

Example:

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

v = np.array([0, 1, 2, 3, 4])

newick = to_newick(v) # '(0,(1,(2,(3,(4,5)6)7)8)9)10;'

v_converted = to_vector(newick) # array([0, 1, 2, 3, 4], dtype=int16)

Optimization

• The opt module contains methods to perform phylogenetic inference using Phylo2Vec vectors
• TODO: include GradME from https://github.com/Neclow/GradME

Example:

from phylo2vec.opt import HillClimbingOptimizer

hc = HillClimbingOptimizer(raxml_cmd="/path/to/raxml-ng_v1.2.0_linux_x86_64/raxml-ng", verbose=True)
v_opt, taxa_dict, losses = hc.fit("/path/to/your_fasta_file.fa")

Citation and other work

@article{phylo2vec,
  title={Phylo2Vec: a vector representation for binary trees},
  author={Penn, Matthew J and Scheidwasser, Neil and Khurana, Mark P and Duch{\^e}ne, David A and Donnelly, Christl A and Bhatt, Samir},
  journal={arXiv preprint arXiv:2304.12693},
  year={2023}
}

• 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