CHANGELOG.md
LICENSE
MANIFEST.in
README.md
pyproject.toml
docs/benchmarking.md
docs/command_reference.md
docs/configuration.md
docs/developer.md
docs/faq.md
docs/index.md
docs/installation.md
docs/interpretation.md
docs/quickstart.md
docs/sensitivity_analysis.md
docs/theory_to_implementation.md
examples/download_real_case_data.py
examples/real_case_1/README.md
examples/real_case_1/housekeeping_gene.fasta
examples/real_case_1/immune_gene.fasta
examples/real_case_1/metadata.tsv
examples/real_case_1/tree.nwk
examples/real_case_1/alignments/housekeeping_gene.fasta
examples/real_case_1/alignments/immune_gene.fasta
examples/real_case_2/README.md
examples/real_case_2/metabolic_gene.fasta
examples/real_case_2/metadata.tsv
examples/real_case_2/receptor_gene.fasta
examples/real_case_2/tree.nwk
examples/real_case_2/alignments/metabolic_gene.fasta
examples/real_case_2/alignments/receptor_gene.fasta
examples/small_demo/README.md
examples/small_demo/geneA.fasta
examples/small_demo/geneB.fasta
examples/small_demo/metadata.tsv
examples/small_demo/tree.nwk
examples/small_demo/alignments/geneA.fasta
examples/small_demo/alignments/geneB.fasta
src/babappa/__init__.py
src/babappa/cli.py
src/babappa/config.py
src/babappa/version.py
src/babappa/workflow.py
src/babappa.egg-info/PKG-INFO
src/babappa.egg-info/SOURCES.txt
src/babappa.egg-info/dependency_links.txt
src/babappa.egg-info/entry_points.txt
src/babappa.egg-info/requires.txt
src/babappa.egg-info/top_level.txt
src/babappa/benchmark/__init__.py
src/babappa/benchmark/comparators.py
src/babappa/benchmark/real_data.py
src/babappa/benchmark/runners.py
src/babappa/benchmark/simulation.py
src/babappa/data/examples/real_case_1/housekeeping_gene.fasta
src/babappa/data/examples/real_case_1/immune_gene.fasta
src/babappa/data/examples/real_case_1/metadata.tsv
src/babappa/data/examples/real_case_1/tree.nwk
src/babappa/data/examples/real_case_1/alignments/housekeeping_gene.fasta
src/babappa/data/examples/real_case_1/alignments/immune_gene.fasta
src/babappa/data/examples/real_case_2/metabolic_gene.fasta
src/babappa/data/examples/real_case_2/metadata.tsv
src/babappa/data/examples/real_case_2/receptor_gene.fasta
src/babappa/data/examples/real_case_2/tree.nwk
src/babappa/data/examples/real_case_2/alignments/metabolic_gene.fasta
src/babappa/data/examples/real_case_2/alignments/receptor_gene.fasta
src/babappa/data/examples/small_demo/geneA.fasta
src/babappa/data/examples/small_demo/geneB.fasta
src/babappa/data/examples/small_demo/metadata.tsv
src/babappa/data/examples/small_demo/tree.nwk
src/babappa/data/examples/small_demo/alignments/geneA.fasta
src/babappa/data/examples/small_demo/alignments/geneB.fasta
src/babappa/features/__init__.py
src/babappa/features/codon.py
src/babappa/features/representation.py
src/babappa/features/smoothing.py
src/babappa/io/__init__.py
src/babappa/io/fasta.py
src/babappa/io/metadata.py
src/babappa/io/newick.py
src/babappa/io/project.py
src/babappa/model/__init__.py
src/babappa/model/bundle.py
src/babappa/model/energy.py
src/babappa/null/__init__.py
src/babappa/null/model.py
src/babappa/null/simulator.py
src/babappa/plots/__init__.py
src/babappa/plots/figures.py
src/babappa/qc/__init__.py
src/babappa/qc/validators.py
src/babappa/report/__init__.py
src/babappa/report/html.py
src/babappa/stats/__init__.py
src/babappa/stats/contributions.py
src/babappa/stats/inference.py
src/babappa/stats/multiple_testing.py
src/babappa/utils/__init__.py
src/babappa/utils/fs.py
src/babappa/utils/logging.py
src/babappa/utils/manifest.py
src/babappa/utils/package_data.py
src/babappa/utils/random.py