CHANGES.txt
LICENSE
MANIFEST.in
README.md
setup.py
./checkm/VERSION
bin/checkm
checkm/DATA_CONFIG
checkm/VERSION
checkm/__init__.py
checkm/aminoAcidIdentity.py
checkm/binStatistics.py
checkm/binTools.py
checkm/checkmData.py
checkm/common.py
checkm/coverage.py
checkm/coverageWindows.py
checkm/customHelpFormatter.py
checkm/defaultValues.py
checkm/fileEntity.py
checkm/genomicSignatures.py
checkm/hmmer.py
checkm/hmmerAligner.py
checkm/hmmerModelParser.py
checkm/logger.py
checkm/main.py
checkm/manifestManager.py
checkm/markerGeneFinder.py
checkm/markerSets.py
checkm/merger.py
checkm/pplacer.py
checkm/prettytable.py
checkm/prodigal.py
checkm/profile.py
checkm/resultsParser.py
checkm/ssuFinder.py
checkm/taxonParser.py
checkm/timeKeeper.py
checkm/treeParser.py
checkm/unbinned.py
checkm/uniqueMarkers.py
checkm/plot/AbstractPlot.py
checkm/plot/__init__.py
checkm/plot/codingDensityPlots.py
checkm/plot/distributionPlots.py
checkm/plot/gcBiasPlots.py
checkm/plot/gcPlots.py
checkm/plot/lengthHistogram.py
checkm/plot/markerGenePosPlot.py
checkm/plot/nxPlot.py
checkm/plot/tetraDistPlots.py
checkm/test/__init__.py
checkm/test/test_aminoAcidIdentity.py
checkm/test/test_binStatistics.py
checkm/test/test_ecoli.py
checkm/test/test_genomicSignatures.py
checkm/test/test_markerSets.py
checkm/test/test_seqUtils.py
checkm/test/test_taxonomyUtils.py
checkm/util/__init__.py
checkm/util/img.py
checkm/util/pfam.py
checkm/util/seqUtils.py
checkm/util/taxonomyUtils.py
checkm_genome.egg-info/PKG-INFO
checkm_genome.egg-info/SOURCES.txt
checkm_genome.egg-info/dependency_links.txt
checkm_genome.egg-info/not-zip-safe
checkm_genome.egg-info/requires.txt
checkm_genome.egg-info/top_level.txt
custom_marker_sets/cpr_43_markers.hmm
custom_marker_sets/cpr_43_markers.xlxs