LICENSE
README.md
pyproject.toml
markerfinder/__init__.py
markerfinder/__main__.py
markerfinder/_cgi_compat.py
markerfinder/_version.py
markerfinder/assertions.py
markerfinder/banner.py
markerfinder/config.py
markerfinder/config_loader.py
markerfinder/exceptions.py
markerfinder/phases.py
markerfinder/pipeline.py
markerfinder/taxonomy.py
markerfinder/validation.py
markerfinder.egg-info/PKG-INFO
markerfinder.egg-info/SOURCES.txt
markerfinder.egg-info/dependency_links.txt
markerfinder.egg-info/entry_points.txt
markerfinder.egg-info/requires.txt
markerfinder.egg-info/top_level.txt
markerfinder/cli/__init__.py
markerfinder/cli/config_build.py
markerfinder/cli/constants.py
markerfinder/cli/logging_setup.py
markerfinder/cli/main.py
markerfinder/cli/parser.py
markerfinder/cli/self_test.py
markerfinder/cli/step_state.py
markerfinder/cli/validation.py
markerfinder/cli/commands/__init__.py
markerfinder/cli/commands/filter.py
markerfinder/cli/commands/infer.py
markerfinder/cli/commands/report.py
markerfinder/cli/commands/scan.py
markerfinder/models/__init__.py
markerfinder/models/alignment.py
markerfinder/models/evidence.py
markerfinder/models/genome.py
markerfinder/models/marker.py
markerfinder/models/pipeline_types.py
markerfinder/models/report.py
markerfinder/models/tree.py
markerfinder/modules/__init__.py
markerfinder/modules/composition.py
markerfinder/modules/consistency_screen.py
markerfinder/modules/hgt_filter.py
markerfinder/modules/hgt_scan.py
markerfinder/modules/mag_optimization.py
markerfinder/modules/marker_selection.py
markerfinder/modules/ortholog_resolver.py
markerfinder/modules/phylogenetic_inference.py
markerfinder/modules/report_generator.py
markerfinder/modules/taxonomy_mustpass.py
markerfinder/utils/__init__.py
markerfinder/utils/concurrency.py
markerfinder/utils/db_versioning.py
markerfinder/utils/dependency_check.py
markerfinder/utils/etree.py
markerfinder/utils/gtdb_tk_markers.py
markerfinder/utils/hgt_utils.py
markerfinder/utils/informative_sites.py
markerfinder/utils/io.py
markerfinder/utils/logging_utils.py
markerfinder/utils/mad_root.py
markerfinder/utils/reference.py
markerfinder/utils/state_codec.py
markerfinder/utils/tree_source.py
markerfinder/utils/tree_utils.py
markerfinder/utils/unmeasured.py