.gitattributes
.gitignore
LICENSE
MANIFEST.in
README.md
Snakefile
pyproject.toml
setup.py
config/config.yaml
config/species_metadata.tsv
envs/babappalign.yaml
envs/clipkit.yaml
envs/codeml.yaml
envs/hyphy.yaml
envs/iqtree.yaml
envs/python.yaml
envs/rbh.yaml
src/babappasnake/__init__.py
src/babappasnake/__main__.py
src/babappasnake/_version.py
src/babappasnake/cli.py
src/babappasnake.egg-info/PKG-INFO
src/babappasnake.egg-info/SOURCES.txt
src/babappasnake.egg-info/dependency_links.txt
src/babappasnake.egg-info/entry_points.txt
src/babappasnake.egg-info/requires.txt
src/babappasnake.egg-info/top_level.txt
src/babappasnake/_bundle/Snakefile
src/babappasnake/_bundle/__init__.py
src/babappasnake/_bundle/config/config.yaml
src/babappasnake/_bundle/config/species_metadata.tsv
src/babappasnake/_bundle/envs/babappalign.yaml
src/babappasnake/_bundle/envs/clipkit.yaml
src/babappasnake/_bundle/envs/codeml.yaml
src/babappasnake/_bundle/envs/hyphy.yaml
src/babappasnake/_bundle/envs/iqtree.yaml
src/babappasnake/_bundle/envs/python.yaml
src/babappasnake/_bundle/envs/rbh.yaml
src/babappasnake/_bundle/workflow/rules/alignment.smk
src/babappasnake/_bundle/workflow/rules/checkpoint.smk
src/babappasnake/_bundle/workflow/rules/codeml.smk
src/babappasnake/_bundle/workflow/rules/hyphy.smk
src/babappasnake/_bundle/workflow/rules/rbh.smk
src/babappasnake/_bundle/workflow/rules/reporting.smk
src/babappasnake/_bundle/workflow/rules/tree.smk
src/babappasnake/_bundle/workflow/scripts/common.py
src/babappasnake/_bundle/workflow/scripts/compile_thresholds.py
src/babappasnake/_bundle/workflow/scripts/parse_hyphy.py
src/babappasnake/_bundle/workflow/scripts/prepare_cds_checkpoint.py
src/babappasnake/_bundle/workflow/scripts/project_protein_trim_to_cds.py
src/babappasnake/_bundle/workflow/scripts/render_codeml_tree.py
src/babappasnake/_bundle/workflow/scripts/root_and_label_tree.py
src/babappasnake/_bundle/workflow/scripts/run_babappalign.py
src/babappasnake/_bundle/workflow/scripts/run_clipkit.py
src/babappasnake/_bundle/workflow/scripts/run_codeml_branchsite.py
src/babappasnake/_bundle/workflow/scripts/run_rbh_species.py
src/babappasnake/_bundle/workflow/scripts/select_codeml_targets.py
src/babappasnake/_bundle/workflow/scripts/select_orthogroup.py
src/babappasnake/_bundle/workflow/scripts/summarize_codeml.py
src/babappasnake/_bundle/workflow/scripts/summarize_iqtree.py
src/babappasnake/_bundle/workflow/scripts/validate_alignment.py
src/babappasnake/_bundle/workflow/scripts/validate_alignment_products.py
src/babappasnake/_bundle/workflow/scripts/validate_user_cds.py
src/babappasnake/_bundle/workflow/scripts/write_executive_summary.py
src/babappasnake/_bundle/workflow/scripts/write_input_manifest.py
tests/test_cli.py
workflow/rules/alignment.smk
workflow/rules/checkpoint.smk
workflow/rules/codeml.smk
workflow/rules/hyphy.smk
workflow/rules/rbh.smk
workflow/rules/reporting.smk
workflow/rules/tree.smk
workflow/scripts/common.py
workflow/scripts/compile_thresholds.py
workflow/scripts/parse_hyphy.py
workflow/scripts/prepare_cds_checkpoint.py
workflow/scripts/project_protein_trim_to_cds.py
workflow/scripts/render_codeml_tree.py
workflow/scripts/root_and_label_tree.py
workflow/scripts/run_babappalign.py
workflow/scripts/run_clipkit.py
workflow/scripts/run_codeml_branchsite.py
workflow/scripts/run_rbh_species.py
workflow/scripts/select_codeml_targets.py
workflow/scripts/select_orthogroup.py
workflow/scripts/summarize_codeml.py
workflow/scripts/summarize_iqtree.py
workflow/scripts/validate_alignment.py
workflow/scripts/validate_alignment_products.py
workflow/scripts/validate_user_cds.py
workflow/scripts/write_executive_summary.py
workflow/scripts/write_input_manifest.py