COPYING
COPYRIGHT
MANIFEST.in
README.md
make
requirements-dev.txt
requirements.txt
setup.cfg
setup.py
PanACoTA/__init__.py
PanACoTA/utils.py
PanACoTA/utils_argparse.py
PanACoTA/utils_pangenome.py
PanACoTA.egg-info/PKG-INFO
PanACoTA.egg-info/SOURCES.txt
PanACoTA.egg-info/dependency_links.txt
PanACoTA.egg-info/entry_points.txt
PanACoTA.egg-info/requires.txt
PanACoTA.egg-info/top_level.txt
PanACoTA/align_module/__init__.py
PanACoTA/align_module/alignment.py
PanACoTA/align_module/get_seqs.py
PanACoTA/align_module/pan_to_pergenome.py
PanACoTA/align_module/post_align.py
PanACoTA/align_module/prt2codon.awk
PanACoTA/annotate_module/__init__.py
PanACoTA/annotate_module/annotation_functions.py
PanACoTA/annotate_module/format_prodigal.py
PanACoTA/annotate_module/format_prokka.py
PanACoTA/annotate_module/general_format_functions.py
PanACoTA/annotate_module/genome_seq_functions.py
PanACoTA/bin/__init__.py
PanACoTA/bin/run_panacota.py
PanACoTA/corepers_module/__init__.py
PanACoTA/corepers_module/persistent_functions.py
PanACoTA/pangenome_module/__init__.py
PanACoTA/pangenome_module/mmseqs_functions.py
PanACoTA/pangenome_module/post_treatment.py
PanACoTA/pangenome_module/protein_seq_functions.py
PanACoTA/prepare_module/__init__.py
PanACoTA/prepare_module/download_genomes_func.py
PanACoTA/prepare_module/filter_genomes.py
PanACoTA/subcommands/__init__.py
PanACoTA/subcommands/align.py
PanACoTA/subcommands/all_modules.py
PanACoTA/subcommands/annotate.py
PanACoTA/subcommands/corepers.py
PanACoTA/subcommands/pangenome.py
PanACoTA/subcommands/prepare.py
PanACoTA/subcommands/tree.py
PanACoTA/tree_module/__init__.py
PanACoTA/tree_module/fastme_func.py
PanACoTA/tree_module/fasttree_func.py
PanACoTA/tree_module/iqtree_func.py
PanACoTA/tree_module/quicktree_func.py
test/__init__.py
test/test_functional/__init__.py
test/test_functional/test_align-parser.py
test/test_functional/test_align.py
test/test_functional/test_all-parser.py
test/test_functional/test_all.py
test/test_functional/test_annote-parser.py
test/test_functional/test_annote.py
test/test_functional/test_corepers-parser.py
test/test_functional/test_corepers.py
test/test_functional/test_pangenome-parser.py
test/test_functional/test_pangenome.py
test/test_functional/test_prepare-parser.py
test/test_functional/test_prepare.py
test/test_functional/test_tree-parser.py
test/test_functional/test_tree.py
test/test_install/__init__.py
test/test_install/test_make_all-installed.py
test/test_install/test_make_barrnap.py
test/test_install/test_make_prodigal.py
test/test_install/test_make_prokka-quicktree.py
test/test_install/test_make_ubuntu.py
test/test_install/utilities.py
test/test_unit/__init__.py
test/test_unit/test_utils-argparse.py
test/test_unit/test_utils-logging.py
test/test_unit/test_utils-pan.py
test/test_unit/test_utils.py
test/test_unit/utilities_for_tests.py
test/test_unit/test_align/__init__.py
test/test_unit/test_align/test_alignment.py
test/test_unit/test_align/test_getseqs.py
test/test_unit/test_align/test_pan2pergenome.py
test/test_unit/test_align/test_postalign.py
test/test_unit/test_annotate/__init__.py
test/test_unit/test_annotate/test_annotation_functions-prodigal.py
test/test_unit/test_annotate/test_annotation_functions-prokka.py
test/test_unit/test_annotate/test_annotation_general.py
test/test_unit/test_annotate/test_format_func.py
test/test_unit/test_annotate/test_format_prodigal.py
test/test_unit/test_annotate/test_format_prokka.py
test/test_unit/test_annotate/test_genome_func.py
test/test_unit/test_corepers/__init__.py
test/test_unit/test_corepers/test_persistent.py
test/test_unit/test_pangenome/__init__.py
test/test_unit/test_pangenome/test_mmseq_func.py
test/test_unit/test_pangenome/test_post_mmseq.py
test/test_unit/test_pangenome/test_protseqfunc.py
test/test_unit/test_prepare/__init__.py
test/test_unit/test_prepare/test_download.py
test/test_unit/test_prepare/test_filter.py
test/test_unit/test_tree/__init__.py
test/test_unit/test_tree/test_fastme.py
test/test_unit/test_tree/test_fasttree.py
test/test_unit/test_tree/test_iqtree.py
test/test_unit/test_tree/test_quicktree.py
test/test_unit/test_tree/utilities.py