├── .github └── workflows │ └── main.yml ├── .gitignore ├── CHANGELOG.md ├── DEVELOPER.md ├── LICENSE ├── Makefile ├── README.md ├── SETUPFILE ├── documentation ├── exampleTutorial │ └── exampleResults │ │ ├── refGenome3clus_allClust_relativeAbund.tab │ │ ├── refGenome3clus_allClust_relativeAbund.tab~ │ │ ├── refGenome3clus_corrGenes-pearson.tsv │ │ ├── refGenome3clus_corrGenes-spearman.tsv │ │ ├── refGenome3clus_detailedSpeciesReport.html │ │ └── refGenome3clus_mann_clustering.tab ├── metaSNV_v2_manual.pdf └── metaSNVv2_manual_20211123.docx ├── metaSNV.py ├── metaSNV_DistDiv.py ├── metaSNV_Filtering.py ├── metaSNV_subpopr.R └── src ├── collapse_coverages.py ├── computeDistances.R ├── computeGenomeCoverage.py ├── createOptimumSplit.py ├── gff2metaSNV_annotation.py ├── profileSamplesUsingGenotypes.R ├── qaTools ├── .gitignore ├── Makefile ├── qaCompute.cpp └── radix.h ├── snpCaller ├── .gitignore ├── Makefile ├── README ├── call_vC.cpp └── gene.h └── subpopr ├── R ├── assessSubpopCompleteness.R ├── clustering.R ├── clusteringStability.R ├── collectSubpopAbunds.R ├── computeSnvFreqStats.R ├── correlateSubpopProfileWithGeneProfiles.R ├── filterSNVpositions.R ├── filterSamples.R ├── getSpeciesTaxonomy.R ├── importSNVresults.R ├── installOrLoadPackages.R ├── parseMotu2Profile.R ├── profileSubpops.R ├── psClusterStats.R ├── renderReports.R ├── rmNAsfromDistMatrix.R ├── runPyScripts.R ├── sampleDistCorrWithCOG.R ├── snvFreqPlot.R ├── summariseClusteringResults.R ├── testPredStrengthMethods.R ├── utils.R ├── varExplainedByClusters.R ├── writeGenotypeFreqs.R ├── writeSubpopAbund.R └── writeSubpopsForAllSamples.R ├── data └── TAXA.NCBI.MOTU.MAP.Rds └── inst ├── convertSNVtoAlleleFreq.py ├── getGenotypingSNVSubset.py └── rmd ├── detailedSpeciesReport.rmd ├── geneContentReport.rmd └── resultsSummary.Rmd /.github/workflows/main.yml: -------------------------------------------------------------------------------- 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