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https://github.com/Ecogenomics/CheckM
08 July 2023, 01:20:46 UTC
History
Tip revision: 106ed78daac7673179ab68dbe02642693a6b9545 authored by dparks1134 on 31 October 2022, 13:52:47 UTC
Support gzipped protein files as input (thanks to alienzj for the PR)
Tip revision: 106ed78
File Mode Size
deprecated
genometreeworkflow
__init__.py -rwxr-xr-x 0 bytes
calculateBounds.py -rwxr-xr-x 7.2 KB
calculateBoundsTD.py -rwxr-xr-x 5.9 KB
calculateConservativeMarkerGenes.py -rwxr-xr-x 4.6 KB
classTree.py -rwxr-xr-x 3.2 KB
classTreeInternalNodeMetadata.py -rwxr-xr-x 2.7 KB
createMarketSetPlots.py -rwxr-xr-x 181 bytes
createSelectedMarkerSetMapping.py -rwxr-xr-x 3.8 KB
createTaxonomicSpecificMarkerSets.py -rwxr-xr-x 10.4 KB
distributionDeltaCodingDensity.py -rwxr-xr-x 8.1 KB
distributionDeltaGC.py -rwxr-xr-x 7.2 KB
distributionDeltaTetraDiff.py -rwxr-xr-x 6.8 KB
evaluatePfamTigrfamHMMs.py -rwxr-xr-x 13.7 KB
evaluateProdigal.py -rwxr-xr-x 10.7 KB
findCircularSeqs.py -rwxr-xr-x 4.7 KB
geneCountDict.py -rwxr-xr-x 3.0 KB
genomeCharacteristics.py -rwxr-xr-x 14.0 KB
genomeTreeWorkflow.py -rwxr-xr-x 11.0 KB
getHMMs.py -rwxr-xr-x 4.1 KB
getMarkerGeneHMMs.py -rwxr-xr-x 4.5 KB
identifyColocatedGenes.py -rwxr-xr-x 4.8 KB
identifyCompleteGenomes.py -rwxr-xr-x 9.0 KB
identifyDegenerateGenomes.py -rwxr-xr-x 6.1 KB
identifyGeneLossAndDuplication.py -rwxr-xr-x 7.3 KB
identifyLineageStability.py -rwxr-xr-x 5.3 KB
markerGeneCorrelation.py -rwxr-xr-x 4.8 KB
markerSetLOO.py -rwxr-xr-x 5.8 KB
markerSetSelection.py -rwxr-xr-x 16.2 KB
markerSetSize.py -rwxr-xr-x 3.8 KB
markerSetSizes.py -rwxr-xr-x 4.0 KB
markerSetStability.py -rwxr-xr-x 8.2 KB
markerSetStabilityTest.py -rwxr-xr-x 7.1 KB
markerSetTest.py -rwxr-xr-x 6.2 KB
plotMarkerSetDistribution.py -rwxr-xr-x 5.7 KB
plotScaffoldLenVsMarkers.py -rwxr-xr-x 7.7 KB
pruneTree.py -rwxr-xr-x 3.1 KB
qcGenomes.py -rwxr-xr-x 10.0 KB
runGenomeSigDist.py -rwxr-xr-x 3.4 KB
runMarkerSetLOO.py -rwxr-xr-x 131 bytes
simCompare.py -rwxr-xr-x 21.4 KB
simCompareDiffPlot.py -rwxr-xr-x 8.4 KB
simComparePlots.py -rwxr-xr-x 32.7 KB
simEvaluateBias.py -rwxr-xr-x 13.2 KB
simEvaluateBiasHistograms.py -rwxr-xr-x 5.5 KB
simInferBestMarkerSet.py -rwxr-xr-x 9.7 KB
simLineageSpecificMarkerSets.py -rwxr-xr-x 6.4 KB
simMarkerGenesVsMarkerSet.py -rwxr-xr-x 5.9 KB
simTiming.py -rwxr-xr-x 9.9 KB
simulation.py -rwxr-xr-x 16.2 KB
simulationScaffoldsByLength.py -rwxr-xr-x 18.5 KB
simulationScaffoldsRandom.py -rwxr-xr-x 18.3 KB
taxonomicTreeWorkflow.py -rwxr-xr-x 17.2 KB
tigr2pfam.py -rwxr-xr-x 5.8 KB
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