.editorconfig
.gitattributes
.gitignore
CHANGELOG.md
CITATION.cff
CONTRIBUTING.md
LICENSE
MANIFEST.in
PUBLISHING.md
README.md
SECURITY.md
VALIDATION_REPORT.md
pyproject.toml
.github/dependabot.yml
.github/pull_request_template.md
.github/ISSUE_TEMPLATE/bug_report.yml
.github/ISSUE_TEMPLATE/feature_request.yml
.github/workflows/ci.yml
.github/workflows/codeql.yml
.github/workflows/release-build.yml
docs/algorithm.md
docs/branch-selection.md
docs/input-formats.md
docs/interpretation.md
docs/validation.md
docs/workflow-integration.md
docs/code-walkthrough/README.md
docs/code-walkthrough/v0.1.0a1/00-execution-map.md
docs/code-walkthrough/v0.1.0a1/01-entry-points-and-cli.md
docs/code-walkthrough/v0.1.0a1/02-models-errors-and-utilities.md
docs/code-walkthrough/v0.1.0a1/03-transposed-nexus-parser.md
docs/code-walkthrough/v0.1.0a1/04-newick-parser.md
docs/code-walkthrough/v0.1.0a1/05-tree-operations-rooting-and-selection.md
docs/code-walkthrough/v0.1.0a1/06-parsimony-reconstruction.md
docs/code-walkthrough/v0.1.0a1/07-branch-analysis.md
docs/code-walkthrough/v0.1.0a1/08-validation-provenance-and-writing.md
docs/code-walkthrough/v0.1.0a1/09-test-to-code-map.md
docs/code-walkthrough/v0.1.0a1/10-maintenance-observations.md
docs/code-walkthrough/v0.1.0a1/QA-REPORT.md
docs/code-walkthrough/v0.1.0a1/README.md
docs/code-walkthrough/v0.1.0a1/SOURCE-COVERAGE.md
examples/validate_report.py
examples/simple/alignment.nex
examples/simple/clade_tips.txt
examples/simple/tree.nwk
examples/simple/expected/members.txt
examples/simple/expected/report.json
examples/simple/expected/results.tsv
examples/snakemake/Snakefile
examples/snakemake/config.yaml
schemas/README.md
schemas/branchsnv-report.schema.json
src/branchsnv/__init__.py
src/branchsnv/__main__.py
src/branchsnv/analysis.py
src/branchsnv/cli.py
src/branchsnv/errors.py
src/branchsnv/models.py
src/branchsnv/newick.py
src/branchsnv/nexus.py
src/branchsnv/parsimony.py
src/branchsnv/provenance.py
src/branchsnv/util.py
src/branchsnv/validation.py
src/branchsnv/writing.py
src/branchsnv.egg-info/PKG-INFO
src/branchsnv.egg-info/SOURCES.txt
src/branchsnv.egg-info/dependency_links.txt
src/branchsnv.egg-info/entry_points.txt
src/branchsnv.egg-info/top_level.txt
tests/test_analysis.py
tests/test_cli.py
tests/test_newick.py
tests/test_nexus.py
tests/test_parsimony.py
tests/test_process_determinism.py
tests/test_provenance.py
tests/test_regression_faults.py
tests/test_release_metadata.py
tests/test_schema.py
tests/test_selection.py
tests/test_validation.py
tests/test_writing.py
tests/fixtures/ab_tips.txt
tests/fixtures/simple.nex
tests/fixtures/simple.nwk
validation/ak3/README.md
validation/ak3/mrsa_360_tips.txt
validation/ak3/run_validation.sh
validation/ak3/sapi_385_tips.txt
validation/ak3/expected/mrsa_360_results.tsv
validation/ak3/expected/sapi_385_results.tsv