CodonAdaptPy

CodonAdaptPy is a Python package for validated coding-sequence analysis, codon-usage and host-adaptation metrics, comparative statistics, evolutionary diagnostics, phylogenetic context, reproducible reporting, and constrained synonymous sequence design.

CodonAdaptPy workflow from validated coding sequences through four analytical lenses to auditable molecular-evolution evidence

CodonAdaptPy treats codon-usage similarity as descriptive evidence rather than direct proof of expression, replication, virulence, host switching, transmission, or biological fitness. Analyses retain validation decisions, reference provenance, software versions, and deterministic seeds where applicable.

Installation

Install the dependency-free analysis core and command-line interface from PyPI:

python -m pip install CodonAdaptPy

Install all optional Python dependencies with:

python -m pip install "CodonAdaptPy[all]"

For development, clone the repository and use an editable installation:

git clone https://github.com/navduhan/CodonAdaptPy.git
cd CodonAdaptPy
python -m pip install --editable ".[dev,all]"

Phylogenetic workflows also require MAFFT, trimAL, IQ-TREE or FastTree. The supplied environment.yml installs these external programs together with CodonAdaptPy.

User guide

Developer reference

Project information