BRANCHSNV¶

BRANCHSNV is a dependency-free Python command-line tool for interrogating one selected branch of a rooted bacterial phylogeny using a transposed NEXUS SNV matrix.

It reports two properties separately:

• strict clade-exclusive nucleotide markers, defined from the observed tip states; and
• substitutions reconstructed on the focal edge, evaluated across all globally optimal equal-cost Sankoff parsimony reconstructions.

This separation prevents clade exclusivity from being treated as equivalent to substitution placement on a branch.

Installation¶

BRANCHSNV requires Python 3.10 or later.

Install the stable v0.1.0 release from Bioconda:

conda create -n branchsnv branchsnv=0.1.0 \
  --channel conda-forge \
  --channel bioconda \
  --strict-channel-priority
conda activate branchsnv
branchsnv --version

Alternatively, install from PyPI:

python -m pip install branchsnv==0.1.0
branchsnv --version

The immutable tagged source release can also be installed directly:

git clone https://github.com/RhysWhite/branchsnv.git
cd branchsnv
git checkout v0.1.0
python -m pip install .
branchsnv --version

Start here¶

• Input formats: accepted NEXUS and Newick input scope.
• Branch selection: exact descendant sets, MRCA selection, deterministic branch IDs, and rooting.
• Algorithm: clade-exclusivity logic and equal-cost Sankoff reconstruction.
• Interpretation: what BRANCHSNV results do and do not imply.
• Workflow integration: use in reproducible pipelines.
• Validation: production testing and independent publication validation.
• Code walkthrough: line-by-line implementation documentation.

Citation and archival record¶

The stable software release is archived in Zenodo with DOI 10.5281/zenodo.21919038. Citation metadata are also provided in CITATION.cff in the source repository.