LICENSE
README.md
setup.py
gtdbtk/__init__.py
gtdbtk/__main__.py
gtdbtk/ani_rep.py
gtdbtk/classify.py
gtdbtk/cli.py
gtdbtk/decorate.py
gtdbtk/exceptions.py
gtdbtk/infer_ranks.py
gtdbtk/main.py
gtdbtk/markers.py
gtdbtk/misc.py
gtdbtk/relative_distance.py
gtdbtk/reroot_tree.py
gtdbtk/tools.py
gtdbtk/trim_msa.py
gtdbtk.egg-info/PKG-INFO
gtdbtk.egg-info/SOURCES.txt
gtdbtk.egg-info/dependency_links.txt
gtdbtk.egg-info/entry_points.txt
gtdbtk.egg-info/requires.txt
gtdbtk.egg-info/top_level.txt
gtdbtk/biolib_lite/__init__.py
gtdbtk/biolib_lite/common.py
gtdbtk/biolib_lite/custom_help_formatter.py
gtdbtk/biolib_lite/exceptions.py
gtdbtk/biolib_lite/execute.py
gtdbtk/biolib_lite/logger.py
gtdbtk/biolib_lite/newick.py
gtdbtk/biolib_lite/parallel.py
gtdbtk/biolib_lite/prodigal_biolib.py
gtdbtk/biolib_lite/seq_io.py
gtdbtk/biolib_lite/taxonomy.py
gtdbtk/config/__init__.py
gtdbtk/config/config.py
gtdbtk/config/output.py
gtdbtk/external/__init__.py
gtdbtk/external/fastani.py
gtdbtk/external/fasttree.py
gtdbtk/external/hmm_aligner.py
gtdbtk/external/mash.py
gtdbtk/external/pfam_search.py
gtdbtk/external/pplacer.py
gtdbtk/external/prodigal.py
gtdbtk/external/tigrfam_search.py
gtdbtk/external/pypfam/__init__.py
gtdbtk/external/pypfam/HMM/HMMMatch.py
gtdbtk/external/pypfam/HMM/HMMResults.py
gtdbtk/external/pypfam/HMM/HMMResultsIO.py
gtdbtk/external/pypfam/HMM/HMMSequence.py
gtdbtk/external/pypfam/HMM/HMMUnit.py
gtdbtk/external/pypfam/HMM/__init__.py
gtdbtk/external/pypfam/Scan/PfamScan.py
gtdbtk/external/pypfam/Scan/__init__.py
gtdbtk/io/__init__.py
gtdbtk/io/batchfile.py
gtdbtk/io/classify_summary.py
gtdbtk/io/gtdb_radii.py
gtdbtk/io/marker_info.py
gtdbtk/io/pplacer_classification.py
gtdbtk/io/red_dict.py
gtdbtk/io/marker/__init__.py
gtdbtk/io/marker/copy_number.py
gtdbtk/io/marker/tophit.py
gtdbtk/io/prodigal/__init__.py
gtdbtk/io/prodigal/tln_table.py
gtdbtk/io/prodigal/tln_table_summary.py
gtdbtk/model/__init__.py
gtdbtk/model/enum.py
gtdbtk/pipeline/__init__.py
gtdbtk/pipeline/align.py
gtdbtk/pipeline/export_msa.py
gtdbtk/tests/data/genomes/genome_1.fna
gtdbtk/tests/data/genomes/genome_2.fna
gtdbtk/tests/data/genomes/genome_3.fna
tests/__init__.py
tests/common.py
tests/test_classify.py
tests/test_cli.py
tests/test_gtdbtk/__init__.py
tests/test_gtdbtk/test__main__.py
tests/test_gtdbtk/test_main.py
tests/test_gtdbtk/test_markers.py
tests/test_gtdbtk/test_tools.py
tests/test_gtdbtk/test_trim_msa.py
tests/test_gtdbtk/test_biolib_lite/__init__.py
tests/test_gtdbtk/test_biolib_lite/test_common.py
tests/test_gtdbtk/test_biolib_lite/test_newick.py
tests/test_gtdbtk/test_biolib_lite/test_seq_io.py
tests/test_gtdbtk/test_biolib_lite/test_taxonomy.py
tests/test_gtdbtk/test_external/__init__.py
tests/test_gtdbtk/test_external/test_fastani.py
tests/test_gtdbtk/test_io/__init__.py
tests/test_gtdbtk/test_io/test_marker/__init__.py
tests/test_gtdbtk/test_io/test_marker/test_copy_number.py
tests/test_gtdbtk/test_io/test_marker/test_tophit.py
tests/test_gtdbtk/test_io/test_prodigal/__init__.py
tests/test_gtdbtk/test_io/test_prodigal/test_tln_table_summary.py