Bijux Phylogenetics

bijux-phylogenetics combines a substantial phylogenetics runtime with a checked-in evidence program and a maintainer-facing trust surface.

This site helps readers answer three questions directly:

• what the runtime can do today
• what the governed evidence actually supports
• how release claims are kept aligned with code, artifacts, and documentation

flowchart TD
    A[Canonical runtime] --> B[Product handbook]
    A --> C[CLI, Python, and native contracts]
    C --> D[Governed artifacts and reports]
    D --> E[Evidence book]
    F[Maintainer package] --> G[Maintainer handbook]
    B --> H[Users and downstream developers]
    E --> I[Scientific reviewers]
    G --> J[Release and trust stewardship]

Start With The Right Surface

Surface	What it is for
Product handbook	runtime ownership, interfaces, workflows, outputs, and quality reading
Evidence book	governed comparative-study dossiers, bundle IDs, provenance, and bounded study claims
Maintainer handbook	documentation truth, release alignment, artifact hygiene, and public trust stewardship

What The Checked-In Runtime Already Covers

Capability family	Publicly visible depth
Trees	PhyloTree, rootedness, support normalization, topology comparison, clades, MRCA review, tree sets, and rendering
Alignments	FASTA validation, trimming, translation, coding checks, partition-aware handling, and packaged example inputs
Native inference	finite-state likelihood, native maximum-likelihood result objects, supported native Bayesian DNA workflows, and benchmark surfaces
Comparative biology	PGLS, signal, regression interpretation, discrete evolution, diversification, and model-selection reading
Ancestral and parsimony analysis	continuous and discrete reconstruction, uncertainty-ledger outputs, and explicit parsimony families
Datasets and reporting	packaged datasets, study inputs, benchmark corpora, HTML and TSV outputs, manifests, and evidence-linked bundles

Start By Goal

• I want to understand what the runtime owns and which interface I should use. Start with the Phylogenetics product handbook.
• I want to understand what the governed comparative-study record actually proves. Start with the Evidence book.
• I want to understand how the repository keeps documentation and release language honest. Start with the Maintainer handbook.

Reader Routes

flowchart LR
    A[What can I run?] --> B[Product handbook]
    C[What has been checked?] --> D[Evidence book]
    E[Why should I trust the release story?] --> F[Maintainer handbook]

• Read the product handbook when the question is about runtime behavior, package roles, interfaces, workflows, outputs, or validation lanes.
• Read the evidence book when the question is about provenance, bundle IDs, study dossiers, or bounded parity claims.
• Read the maintainer handbook when the question is about narrative alignment, artifact hygiene, metadata truth, or release readiness.

Flagship Starting Points

• Surface selection guide
• Native maximum-likelihood workflows
• Native Bayesian workflows
• Validation lanes
• Evidence book overview
• Maintainer handbook overview

Important Boundary

The code surface is broader than the currently closed evidence surface, and the evidence surface is narrower than the full runtime surface. A feature can be documented and usable without claiming that every surrounding scientific interpretation has already been closed by governed study evidence.