phylogenetic 0.1.2

Short install name for the full Bijux phylogenetics runtime, CLI, and comparative-analysis workflows.

phylogenetic

Compatibility alias package for bijux-phylogenetics.

This distribution installs the canonical phylogenetics runtime under the shorter phylogenetic package and CLI names. It is not a reduced runtime and it is not a fork. It points at the same benchmark, workflow, and reporting surfaces that the canonical package publishes.

Alias Structure At A Glance

• shorter install name
• shorter CLI name
• same canonical runtime behavior

Install

phylogenetic supports Python 3.11 and newer.

python3.11 -m pip install phylogenetic
phylogenetic --help

What You Still Get

Installing the alias package still gives you access to the same documented runtime depth:

Capability family	What carries through the alias
Trees and alignments	inspection, validation, comparison, and preparation workflows
Native runtime	native likelihood and native inference surfaces
Comparative analysis	comparative and ancestral workflows
Reporting	benchmark, workflow, and reporting surfaces
External engines	governed wrapper-backed external-engine workflows

What The Alias Does Not Change

• it does not remove native inference surfaces
• it does not remove comparative, ancestral, or parsimony families
• it does not change the evidence-book or quality reading model
• it does not publish a smaller scientific contract than the canonical package

Choose this package when you want the shorter install and command names while keeping the same public runtime contract.

Choose the canonical bijux-phylogenetics package instead when you want the most explicit package name for notebooks, papers, release notes, or downstream documentation.

Shorter Python Workflow Surface

The alias keeps the same workflow API surface under the shorter phylogenetic.api import path.

from pathlib import Path

from phylogenetic.api import (
    render_report_workflow,
    run_comparative_model_workflow,
    run_sequence_to_tree_workflow,
)

workflow = run_sequence_to_tree_workflow(
    Path("dataset/sequences.fasta"),
    out_dir=Path("artifacts/sequence-to-tree"),
    sequence_type="dna",
)

comparative = run_comparative_model_workflow(
    Path("dataset/tree.nwk"),
    Path("dataset/traits.tsv"),
    response="response",
    predictors=["predictor_one"],
    lambda_value=1.0,
)

report = render_report_workflow(
    tree_path=workflow.output_paths["tree"],
    alignment_path=workflow.output_paths["trimmed_alignment"],
    traits_path=Path("dataset/traits.tsv"),
    metadata_path=Path("dataset/metadata.tsv"),
    out_path=Path("artifacts/sequence-to-tree/report.html"),
)

workflow.write_json(Path("artifacts/sequence-to-tree/workflow.json"))
workflow.write_tsv(Path("artifacts/sequence-to-tree/workflow.tsv"))
comparative.write_tsv(Path("artifacts/comparative-model.tsv"))

Use the alias when you want the shorter import and command surface:

• from phylogenetic.api import ...
• phylogenetic --help

Use the canonical runtime name when you want the most explicit package name in public artifacts, papers, release notes, or downstream documentation:

• from bijux_phylogenetics.api import ...
• bijux-phylogenetics --help

Read This Next

• Runtime product guide
• Runtime architecture
• Surface selection guide
• Artifact consumption guide
• Native Inference And Benchmark Surfaces
• Native maximum-likelihood workflows
• Native Bayesian workflows
• Native benchmark review
• Release review workflow
• Evidence-book guide
• Canonical runtime package on GitHub