LICENSE
MANIFEST.in
README.md
pyproject.toml
babappasnake/__init__.py
babappasnake/cli.py
babappasnake/utils.py
babappasnake.egg-info/PKG-INFO
babappasnake.egg-info/SOURCES.txt
babappasnake.egg-info/dependency_links.txt
babappasnake.egg-info/entry_points.txt
babappasnake.egg-info/requires.txt
babappasnake.egg-info/top_level.txt
babappasnake/scripts/__init__.py
babappasnake/scripts/backtranslate_alignment.py
babappasnake/scripts/compare_alignment_methods.py
babappasnake/scripts/generate_robustness_reports.py
babappasnake/scripts/make_foreground_tree.py
babappasnake/scripts/map_cds_to_proteins.py
babappasnake/scripts/parse_hyphy_foregrounds.py
babappasnake/scripts/prepare_foreground_trees.py
babappasnake/scripts/prepare_pal2nal_inputs.py
babappasnake/scripts/root_tree_outgroup.py
babappasnake/scripts/run_branchsite_batch.py
babappasnake/scripts/run_codeml_asr.py
babappasnake/scripts/run_hyphy.py
babappasnake/scripts/run_rbh_pipeline.py
babappasnake/scripts/strip_terminal_stop_codon.py
babappasnake/scripts/summarize_results.py
babappasnake/scripts/write_waiting_note.py
babappasnake/workflow/Snakefile
babappasnake/workflow/config_template.yaml
tests/test_backtranslate_alignment.py
tests/test_robustness_reports.py
tests/test_run_hyphy.py
tests/test_trim_strategy.py