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CHANGELOG.md
CITATION.cff
LICENCE.txt
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README.md
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pixi.toml
pyproject.toml
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docker/Dockerfile.in
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docker/lambda_phage.fna
docker/test.fna
docs/AGENTS.md
docs/FAQ.md
docs/Glossary.md
docs/Installation.md
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docs/Lyrebird.md
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extras/assign_gtdb_taxonomy_to_gtdb_genomes.py
extras/condensed_profile_to_biobox.py
extras/gtdb_vs_gtdb_query_parser.py
extras/inter_lineage_distance_calculator.py
extras/merge_metapackages.py
extras/metapackage_slim_for_no_assign_taxonomy.py
extras/singlem_an_sra.py
extras/sra_input_generator.py
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extras/update_metapackage/hmms_and_names
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extras/update_metapackage/scripts/get_matches_no_dup.py
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singlem/__init__.py
singlem/__main__.py
singlem/appraisal_result.py
singlem/appraiser.py
singlem/archive_otu_table.py
singlem/chainsaw.py
singlem/checkm2.py
singlem/clusterer.py
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singlem/diamond_parser.py
singlem/diamond_spkg_searcher.py
singlem/genome_fasta_mux.py
singlem/genome_size.py
singlem/graftm_result.py
singlem/hmm_logo.py
singlem/kingfisher_sra.py
singlem/known_otu_table.py
singlem/lyrebird.py
singlem/main.py
singlem/metagenome_otu_finder.py
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singlem/metapackage_read_name_store.py
singlem/ordered_set.py
singlem/orf_length_checker.py
singlem/otu_table.py
singlem/otu_table_collection.py
singlem/otu_table_entry.py
singlem/package_creator.py
singlem/pipe.py
singlem/pipe_sequence_extractor.py
singlem/pipe_taxonomy_assigner_by_query.py
singlem/placement_parser.py
singlem/querier.py
singlem/query_formatters.py
singlem/rarefier.py
singlem/read_fraction.py
singlem/regenerator.py
singlem/renew.py
singlem/run_via_os_system.py
singlem/sequence_classes.py
singlem/sequence_database.py
singlem/sequence_extractor.py
singlem/singlem_database_models.py
singlem/singlem_package.py
singlem/strain_summariser.py
singlem/streaming_hmm_search_result.py
singlem/summariser.py
singlem/supplement.py
singlem/taxonomy.py
singlem/taxonomy_bihash.py
singlem/trim_package_hmms.py
singlem/utils.py
singlem/version.py
singlem.egg-info/PKG-INFO
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singlem.egg-info/dependency_links.txt
singlem.egg-info/entry_points.txt
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singlem/biolib_lite/__init__.py
singlem/biolib_lite/common.py
singlem/biolib_lite/custom_help_formatter.py
singlem/biolib_lite/exceptions.py
singlem/biolib_lite/execute.py
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singlem/biolib_lite/newick.py
singlem/biolib_lite/parallel.py
singlem/biolib_lite/prodigal_biolib.py
singlem/biolib_lite/seq_io.py
singlem/biolib_lite/taxonomy.py