Getting Started

Install OrthoEvolution and make sure that the package works before an analysis.

A comparative-genetics analysis moves from candidate orthologs to sequences, alignments, and trees. OrthoEvolution coordinates these steps. External scientific programs run tasks such as BLAST searches and sequence alignment.

Requirements

OrthoEvolution supports Python 3.11 through 3.14. Before you begin, identify the external programs that your workflow uses. The Python package does not install these programs:

  • NCBI BLAST+ for local similarity searches
  • Clustal Omega, GUIDANCE2, or PAL2NAL for supported alignment workflows
  • PAML, PhyML, IQ-TREE, Phylip, or ETE for supported phylogenetic workflows
  • PBS or Slurm commands when submitting work to a cluster

If your workflow uses an external program, install it before you start the analysis. The import test checks Python only. It does not test external programs or reference databases.

Before you create the environment, install uv.

Install from PyPI

uv venv --python 3.14 .venv
uv pip install --python .venv/bin/python OrthoEvol

Install from source

git clone https://github.com/datasnakes/OrthoEvolution.git
cd OrthoEvolution
uv venv --python 3.14 .venv
uv pip install --python .venv/bin/python -e .

Verify the installation

.venv/bin/python -c "import OrthoEvol; print(OrthoEvol.__name__)"

This command makes sure that Python can import the package. It does not test external programs, network access, database contents, or a scheduler configuration.

Choose a workflow