OrthoEvolution

OrthoEvolution is a Python package for reproducible comparative evolutionary genetics, with a focus on ortholog inference, sequence analysis, and phylogenetic workflows.

Current version: 1.0.0

Table of Contents

• Project Background
• Core Capabilities
• Install & Setup
• Usage
• Documentation and Examples
• Testing
• Contributing
• Citation
• License
• Authors

Project Background

OrthoEvolution supports the inference and analysis of orthologous genes using NCBI BLAST, multiple-sequence alignment strategies, and phylogenetic tools. It organizes these steps into reusable workflows so researchers can manage large comparative-genetics datasets and reproduce their analyses.

The package is organized around four major areas:

• Orthologs provides ortholog inference, alignment, and phylogenetic tools.
• Manager creates and coordinates repositories, projects, databases, and research datasets.
• Tools provides reusable utilities for data retrieval, parallel execution, logging, and cluster workloads.
• Cookies provides project and website templates.

For additional scientific context, see this related comparative-genetics paper.

Core Capabilities

• Infer candidate orthologs and generate post-BLAST reports.
• Retrieve NCBI datasets and preformatted BLAST databases.
• Prepare and filter nucleotide or protein sequence alignments.
• Support phylogenetic workflows involving PAML, PhyML, IQ-TREE, Phylip, and ETE.
• Create consistent directory structures for comparative-genetics projects.
• Configure local, parallel, PBS, and Slurm-oriented workloads.

Some workflows call external scientific programs or remote services. Install the required BLAST, alignment, or phylogenetic software for the specific workflow you intend to run.

Install & Setup

OrthoEvolution supports Python 3.11 and 3.12. A virtual environment keeps its dependencies separate from other Python projects.

Install from PyPI

python3.11 -m venv .venv
source .venv/bin/activate
python -m pip install --upgrade pip
python -m pip install OrthoEvol

Install from source

git clone https://github.com/datasnakes/OrthoEvolution.git
cd OrthoEvolution
python3.11 -m venv .venv
source .venv/bin/activate
python -m pip install --upgrade pip
python -m pip install .

Install for development

git clone https://github.com/datasnakes/OrthoEvolution.git
cd OrthoEvolution
python3.11 -m venv .venv
source .venv/bin/activate
python -m pip install --upgrade pip
python -m pip install -e ".[test]"

Usage

Run a preconfigured local BLAST workflow

from OrthoEvol.Orthologs.Blast import OrthoBlastN

gpcr_blastn = OrthoBlastN(
    project="orthology-gpcr",
    method=1,
    save_data=True,
    acc_file="gpcr.csv",
    copy_from_package=True,
)
gpcr_blastn.run()

This workflow requires a compatible local BLAST installation and database.

Create a comparative-genetics project

from OrthoEvol.Manager.management import ProjectManagement

project_manager = ProjectManagement(
    repo="test-repo",
    user=None,
    project="test-project",
    research=None,
    research_type="comparative_genetics",
    new_project=True,
)

Download an NCBI BLAST database

from pathlib import Path

from OrthoEvol.Tools.ftp import NcbiFTPClient

ncbi_ftp = NcbiFTPClient(email="researcher@example.org")
ncbi_ftp.getblastdb(
    database_name="refseq_rna",
    download_path=Path("databases"),
    v5=True,
)

NCBI database downloads require network access and can use substantial disk space. Choose the destination and database deliberately before starting a transfer.

Documentation and Examples

• Read the OrthoEvolution documentation for module and API details.
• Browse the examples for scripts, example data, and interface prototypes.
• Report problems or request enhancements through GitHub Issues.

Testing

Install the development dependencies and run the test suite through the active virtual environment:

python -m pip install -e ".[test]"
python -m pytest tests/

The continuous-integration workflow runs the suite on Python 3.11 and 3.12.

Contributing

Contributions are welcome. Create a focused branch, include tests and documentation where appropriate, and review the contributing guidelines before opening a pull request.

Citation

If you use OrthoEvolution in research, please cite the software:

Gilmore, R., & Hutchins, S. D. (2026). OrthoEvolution (Version 1.0.0) [Computer software]. Zenodo. https://doi.org/10.5281/zenodo.17796234

OrthoEvolution builds on the work of the Biopython community. We thank its developers and contributors and ask users to cite Biopython when it supports their analyses:

Cock, P. J. A., et al. (2009). Biopython: Freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics, 25(11), 1422–1423. https://doi.org/10.1093/bioinformatics/btp163

License

OrthoEvolution is distributed under the MIT License.

Authors

OrthoEvolution was created and is maintained by the Datasnakes:

• Rob Gilmore
• Shaurita D. Hutchins