Research software

Methods that expose their assumptions.

Focused command-line tools for genomic steps where the exact input, exact transformation and uncertainty need to remain inspectable.

Released · v0.1.1

NEXCISION

Removes coordinate-labelled rows from transposed NEXUS matrices without silently changing unrelated content.

Dependency-free Python
Deterministic JSON provenance
SHA-256 checksums
Independent oracle, synthetic, malformed-input and fault-injection validation
105/105 scalability benchmark runs completed

Reachupdated monthly with boast

Automated metrics activate after the first scheduled snapshot.

Publication attention

Code Docs Preprint Validation

Install / discover: PyPI · Bioconda · bio.tools
Archive: Zenodo

Released · v0.1.0

BRANCHSNV

Separates two branch-level properties that are often conflated: strict clade exclusivity and a substitution reconstructed on the focal phylogenetic edge.

Dependency-free Python
Rooted-tree branch analysis
Strict fixed-exclusive marker classification
Equal-cost Sankoff parsimony
All optimal focal-edge state pairs retained
Deterministic reports and SHA-256 input provenance

Reachupdated monthly with boast

Automated metrics activate after the first scheduled snapshot.

Code DocsPreprint soonValidation

Install / discover: PyPI · Bioconda · bio.tools
Archive: Zenodo

Validation

Independent checks, adversarial cases, reproducible benchmarks.

The software repositories preserve the evidence needed to test the implementation: independent expected results, deliberately faulted alternatives, boundary cases, checksums and performance runs.