Repository Scope and Limits

This repository owns a serious phylogenetics runtime, but it still has clear limits. Those limits matter because the public docs should explain what the repository can support today without borrowing credibility from future work.

flowchart LR
    A[Repository scope] --> B[Owned runtime]
    A --> C[Wrapper-backed workflows]
    A --> D[Evidence-linked reporting]
    A --> E[Explicit limits]

In Scope

• deterministic tree and alignment workflows
• native finite-state likelihood and supported native inference contracts
• comparative and ancestral analysis over governed inputs
• adapter surfaces that orchestrate external engines honestly
• evidence-linked reporting and publication-style artifact packaging

Out Of Scope

• claiming broader scientific validation than the evidence-book proves
• treating every wrapper-backed workflow as if it had already been reimplemented locally
• describing narrow native inference ownership as if it already covered every model family and every phylogenetic workflow in the repository
• hiding unresolved runtime or evidence limits behind marketing language

What The Limits Protect

These limits protect three parts of the public story:

• users can still see substantial runtime depth without being misled about closure
• reviewers can tell which surfaces are owned, wrapped, benchmarked, or study-backed
• releases can stay credible because the docs avoid implying a larger scientific claim than the evidence-book supports

Why This Matters

Phylogenetics is a domain where people will naturally overread polished output. This repository has to resist that. Public documentation is part of the trust contract, not just an introduction layer.