.readthedocs.yaml
LICENSE.txt
MANIFEST.in
README.md
VERSION
ppanggolin_env.yaml
pyproject.toml
setup.py
.github/workflows/black_lint.yml
.github/workflows/check_doc.yml
.github/workflows/check_recipes.yml
.github/workflows/main.yml
.github/workflows/pypi.yml
PPanGGOLiN.egg-info/PKG-INFO
PPanGGOLiN.egg-info/SOURCES.txt
PPanGGOLiN.egg-info/dependency_links.txt
PPanGGOLiN.egg-info/entry_points.txt
PPanGGOLiN.egg-info/requires.txt
PPanGGOLiN.egg-info/top_level.txt
ppanggolin/__init__.py
ppanggolin/edge.py
ppanggolin/geneFamily.py
ppanggolin/genetic_codes.py
ppanggolin/genome.py
ppanggolin/main.py
ppanggolin/metadata.py
ppanggolin/pangenome.py
ppanggolin/region.py
ppanggolin/utils.py
ppanggolin/RGP/__init__.py
ppanggolin/RGP/genomicIsland.py
ppanggolin/RGP/rgp_cluster.py
ppanggolin/RGP/spot.py
ppanggolin/align/__init__.py
ppanggolin/align/alignOnPang.py
ppanggolin/annotate/__init__.py
ppanggolin/annotate/annotate.py
ppanggolin/annotate/synta.py
ppanggolin/annotate/rRNA_DB/RF00001.cm
ppanggolin/annotate/rRNA_DB/RF00177.cm
ppanggolin/annotate/rRNA_DB/RF01959.cm
ppanggolin/annotate/rRNA_DB/RF02540.cm
ppanggolin/annotate/rRNA_DB/RF02541.cm
ppanggolin/annotate/rRNA_DB/rRNA_arch.cm
ppanggolin/annotate/rRNA_DB/rRNA_arch.cm.i1f
ppanggolin/annotate/rRNA_DB/rRNA_arch.cm.i1i
ppanggolin/annotate/rRNA_DB/rRNA_arch.cm.i1m
ppanggolin/annotate/rRNA_DB/rRNA_arch.cm.i1p
ppanggolin/annotate/rRNA_DB/rRNA_bact.cm
ppanggolin/annotate/rRNA_DB/rRNA_bact.cm.i1f
ppanggolin/annotate/rRNA_DB/rRNA_bact.cm.i1i
ppanggolin/annotate/rRNA_DB/rRNA_bact.cm.i1m
ppanggolin/annotate/rRNA_DB/rRNA_bact.cm.i1p
ppanggolin/cluster/__init__.py
ppanggolin/cluster/cluster.py
ppanggolin/context/__init__.py
ppanggolin/context/searchGeneContext.py
ppanggolin/figures/__init__.py
ppanggolin/figures/draw_spot.py
ppanggolin/figures/drawing.py
ppanggolin/figures/tile_plot.py
ppanggolin/figures/ucurve.py
ppanggolin/formats/__init__.py
ppanggolin/formats/readBinaries.py
ppanggolin/formats/writeAnnotations.py
ppanggolin/formats/writeBinaries.py
ppanggolin/formats/writeFlatGenomes.py
ppanggolin/formats/writeFlatMetadata.py
ppanggolin/formats/writeFlatPangenome.py
ppanggolin/formats/writeMSA.py
ppanggolin/formats/writeMetadata.py
ppanggolin/formats/writeSequences.py
ppanggolin/formats/write_proksee.py
ppanggolin/graph/__init__.py
ppanggolin/graph/makeGraph.py
ppanggolin/info/__init__.py
ppanggolin/info/info.py
ppanggolin/meta/__init__.py
ppanggolin/meta/meta.py
ppanggolin/metrics/__init__.py
ppanggolin/metrics/fluidity.py
ppanggolin/metrics/metrics.py
ppanggolin/mod/__init__.py
ppanggolin/mod/module.py
ppanggolin/nem/__init__.py
ppanggolin/nem/partition.py
ppanggolin/nem/rarefaction.py
ppanggolin/nem/NEM/genmemo.c
ppanggolin/nem/NEM/genmemo.h
ppanggolin/nem/NEM/lib_io.c
ppanggolin/nem/NEM/lib_io.h
ppanggolin/nem/NEM/nem_alg.c
ppanggolin/nem/NEM/nem_alg.h
ppanggolin/nem/NEM/nem_exe.c
ppanggolin/nem/NEM/nem_exe.h
ppanggolin/nem/NEM/nem_hlp.c
ppanggolin/nem/NEM/nem_hlp.h
ppanggolin/nem/NEM/nem_mod.c
ppanggolin/nem/NEM/nem_mod.h
ppanggolin/nem/NEM/nem_nei.c
ppanggolin/nem/NEM/nem_nei.h
ppanggolin/nem/NEM/nem_rnd.c
ppanggolin/nem/NEM/nem_rnd.h
ppanggolin/nem/NEM/nem_stats.pyx
ppanggolin/nem/NEM/nem_typ.h
ppanggolin/nem/NEM/nem_ver.c
ppanggolin/nem/NEM/nem_ver.h
ppanggolin/projection/__init__.py
ppanggolin/projection/projection.py
ppanggolin/utility/__init__.py
ppanggolin/utility/utils.py
ppanggolin/workflow/__init__.py
ppanggolin/workflow/all.py
ppanggolin/workflow/panModule.py
ppanggolin/workflow/panRGP.py
ppanggolin/workflow/workflow.py
tests/pytest.ini
tests/test_edge.py
tests/test_genefamily.py
tests/test_genome.py
tests/test_metadata.py
tests/test_pangenome.py
tests/test_region.py
tests/align/test_align.py
tests/annotate/test_annotate.py
tests/context/test_context.py
tests/formats/test_writeFlatGenomes.py
tests/region/test_genomicIsland.py
tests/region/test_rgp_cluster.py
tests/utils/test_utilities.py