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 · Bioconda

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 Preprint Validation

Alpha research software

BRANCHSNV

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

Rooted-tree branch analysis
Strict fixed-exclusive marker classification
Equal-cost Sankoff parsimony
All optimal focal-edge state pairs retained
Deterministic reports and input checksums

Active research project. Release information will be expanded alongside the manuscript.

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.