.dockerignore
.zenodo.json
CHANGELOG.md
CITATION.cff
Dockerfile
LICENSE
MANIFEST.in
README.md
RELEASE_VALIDATION.md
RESEARCHER_VALIDATION.md
environment.yml
pyproject.toml
setup.py
docs/BENCHMARK.md
docs/FUNCTIONAL_BENCHMARK.md
docs/INPHARED.md
docs/annotation-naming.md
docs/annotation-workflows.md
docs/architecture-phase-a.md
docs/database-policy.md
docs/databases.md
docs/evidence-framework.md
docs/genbank-submission.md
docs/gui.md
docs/installation.md
docs/limitations.md
docs/next-generation-evidence-engine.md
docs/release-checklist.md
docs/researcher-readiness.md
docs/v1.2-biological-feature-freeze.md
docs/v1.2-consensus-gene-model-policy.md
docs/v1.2-development-environment.md
docs/v1.2-finalization-policy.md
docs/v1.2-gene-model-adjudication.md
docs/v1.2-gene-model-provider-architecture.md
docs/v1.2-prodigal-gv-provider.md
docs/v1.2-pyrodigal-provider.md
docs/v1.2-reconciliation-policy.md
docs/v1.2-rna-phage-support.md
docs/v1.2-segmented-performance-analysis.md
docs/validation-protocol.md
docs/benchmark_v1.2/README.md
docs/benchmark_v1.2/figures/functional_yield.pdf
docs/benchmark_v1.2/figures/functional_yield.png
docs/benchmark_v1.2/figures/functional_yield.svg
docs/benchmark_v1.2/figures/per_genome_strict_f1.pdf
docs/benchmark_v1.2/figures/per_genome_strict_f1.png
docs/benchmark_v1.2/figures/per_genome_strict_f1.svg
docs/benchmark_v1.2/figures/prediction_category_composition.pdf
docs/benchmark_v1.2/figures/prediction_category_composition.png
docs/benchmark_v1.2/figures/prediction_category_composition.svg
docs/benchmark_v1.2/figures/strict_vs_relaxed_f1.pdf
docs/benchmark_v1.2/figures/strict_vs_relaxed_f1.png
docs/benchmark_v1.2/figures/strict_vs_relaxed_f1.svg
docs/benchmark_v1.2/scripts/make_figures.py
docs/benchmark_v1.2/tables/functional_yield_by_genome.tsv
docs/benchmark_v1.2/tables/functional_yield_totals.tsv
docs/benchmark_v1.2/tables/phagemine_vs_prokka_count_difference.tsv
docs/benchmark_v1.2/tables/prediction_category_counts.tsv
docs/benchmark_v1.2/tables/reference_provenance.tsv
docs/benchmark_v1.2/tables/strict_relaxed_metrics.tsv
docs/images/phagemine-gui/annotation-development.png
docs/images/phagemine-gui/home-development.png
docs/releases/v1.3.0.md
docs/releases/v1.3.1.md
examples/demo_phage.fasta
examples/sequencing_provenance_ont.json
examples/submission_metadata.json
packaging/bioconda/post-link.sh
packaging/bioconda/recipe/meta.yaml
src/phagemine/__init__.py
src/phagemine/__main__.py
src/phagemine/adjudication.py
src/phagemine/alternative_evidence.py
src/phagemine/annotation.py
src/phagemine/annotation_labels.py
src/phagemine/artifact_ops.py
src/phagemine/batch.py
src/phagemine/benchmark.py
src/phagemine/cli.py
src/phagemine/compare.py
src/phagemine/conflict_review.py
src/phagemine/context.py
src/phagemine/curated_benchmark.py
src/phagemine/curation.py
src/phagemine/database_health.py
src/phagemine/database_installer.py
src/phagemine/discovery.py
src/phagemine/evidence.py
src/phagemine/evidence_engine.py
src/phagemine/external_annotation.py
src/phagemine/family.py
src/phagemine/family_compare.py
src/phagemine/family_enrichment.py
src/phagemine/family_external.py
src/phagemine/family_priority.py
src/phagemine/figures.py
src/phagemine/functional_benchmark.py
src/phagemine/fusion.py
src/phagemine/genbank.py
src/phagemine/gene_callers.py
src/phagemine/gene_model_selection.py
src/phagemine/gene_models.py
src/phagemine/gene_prediction.py
src/phagemine/genome.py
src/phagemine/genome_representation.py
src/phagemine/hallmarks.py
src/phagemine/hmmer_chunking.py
src/phagemine/inphared.py
src/phagemine/io.py
src/phagemine/mining.py
src/phagemine/model_adjudication.py
src/phagemine/models.py
src/phagemine/operational_validation.py
src/phagemine/pfam.py
src/phagemine/phrogs.py
src/phagemine/pipeline.py
src/phagemine/pooled.py
src/phagemine/preflight.py
src/phagemine/progress.py
src/phagemine/quality.py
src/phagemine/reconciliation.py
src/phagemine/reconciliation_engine.py
src/phagemine/reporting.py
src/phagemine/reproducibility.py
src/phagemine/resources.py
src/phagemine/resume.py
src/phagemine/review.py
src/phagemine/review_priority.py
src/phagemine/rna_features.py
src/phagemine/search_cache.py
src/phagemine/sentinel_diagnostic.py
src/phagemine/sequencing_provenance.py
src/phagemine/stage_dag.py
src/phagemine/stage_resume.py
src/phagemine/submission_revision.py
src/phagemine/swissprot.py
src/phagemine/triage.py
src/phagemine/validation.py
src/phagemine/vog.py
src/phagemine/workflow_cli.py
src/phagemine.egg-info/PKG-INFO
src/phagemine.egg-info/SOURCES.txt
src/phagemine.egg-info/dependency_links.txt
src/phagemine.egg-info/entry_points.txt
src/phagemine.egg-info/requires.txt
src/phagemine.egg-info/top_level.txt
src/phagemine/gui/__init__.py
src/phagemine/gui/app.py
src/phagemine/gui/launcher.py
src/phagemine/gui/services/__init__.py
src/phagemine/gui/services/execution.py
src/phagemine/gui/services/results.py
src/phagemine/gui/services/status.py
tests/test_accuracy_review.py
tests/test_annotation_workflows.py
tests/test_automatic_pyrodigal_gv.py
tests/test_batch_failure_reporting.py
tests/test_benchmark_integrity.py
tests/test_database_installer.py
tests/test_evidence_engine.py
tests/test_fresh_benchmark.py
tests/test_full_system_benchmark.py
tests/test_functional_benchmark.py
tests/test_gene_callers.py
tests/test_gene_model_selection.py
tests/test_gene_models.py
tests/test_gui.py
tests/test_gui_app.py
tests/test_inphared.py
tests/test_model_adjudication.py
tests/test_naming_policy.py
tests/test_ncbi_presubmission.py
tests/test_next_steps.py
tests/test_packaging_pyrodigal_gv.py
tests/test_phagemine.py
tests/test_phrogs_pyhmmer.py
tests/test_preflight.py
tests/test_python_compatibility.py
tests/test_reconciliation_engine.py
tests/test_release_metadata.py
tests/test_release_publication.py
tests/test_release_v12.py
tests/test_sentinel_diagnostic.py
tests/test_small_genome_fallback.py
tests/test_stage_dag_pooled.py
tests/test_step7b_provider_policy.py
tests/test_step8_rna.py
tests/test_step9a_performance.py
tests/test_swissprot_metadata_cache.py
tests/test_triage_report.py
tests/test_validation.py
tools/publish_verified_release.py
tools/smoke_installed.py