├── .Rbuildignore ├── .gitignore ├── .travis.yml ├── DESCRIPTION ├── NAMESPACE ├── R ├── LDgenepop.R ├── RcppExports.R ├── TiTvRatio.R ├── alleleFreqs.R ├── alleleSplit.R ├── allelicRichness.R ├── arlequin.R ├── as.data.frame.gtypes.R ├── as.multidna.R ├── baseFreqs.R ├── clumpp.R ├── createConsensus.R ├── df2gtypes.R ├── diagnosability.R ├── dupGenotypes.R ├── evanno.R ├── expandHaplotypes.R ├── fasta.R ├── fixedDifferences.R ├── fixedSites.R ├── freq2GenData.R ├── fsc.input.R ├── fscRead.R ├── fscRun.R ├── fscWrite.R ├── fusFs.R ├── gelato.R ├── genepop.R ├── gtypes.accessors.R ├── gtypes.class.R ├── gtypes.initialize.R ├── gtypes.show.R ├── gtypes.summary.R ├── gtypes2genind.R ├── gtypes2genlight.R ├── gtypes2loci.R ├── gtypes2phyDat.R ├── gtypes2rfDF.R ├── gtypesRF.R ├── heterozygosity.R ├── hweTest.R ├── is.gtypes.R ├── iupac.R ├── jackHWE.R ├── labelHaplotypes.R ├── landscape2gtypes.R ├── ldNe.R ├── lowFreqSubs.R ├── mRatio.R ├── maf.R ├── mafft.R ├── maverickRun.R ├── mega.R ├── microhaplot2rubias.R ├── mostDistantSequences.R ├── mostRepresentativeSequences.R ├── neiDa.R ├── nucleotideDivergence.R ├── nucleotideDiversity.R ├── numAlleles.R ├── numGenotyped.R ├── numMissing.R ├── permuteStrata.R ├── phase.R ├── popGenEqns.R ├── popStructTest.R ├── privateAlleles.R ├── propUniqueAlleles.R ├── qual2prob.R ├── readGenData.R ├── removeUnusedSequences.R ├── sequence2gtypes.R ├── sequenceLikelihoods.R ├── sequenceRF.R ├── sfs.R ├── sharedLoci.R ├── simGammaHaps.R ├── strataG-internal.R ├── strataG-package.R ├── strataSplit.R ├── stratify.R ├── structure.R ├── structurePlot.R ├── summarizeAll.R ├── summarizeInds.R ├── summarizeLoci.R ├── summarizeSeqs.R ├── sysdata.rda ├── tajimasD.R ├── theta.R ├── trimNs.R ├── variableSites.R ├── write.nexus.snapp.R ├── writeGtypes.R └── zygosity.R ├── README.md ├── appveyor.yml ├── data ├── bowhead.snp.position.rda ├── bowhead.snps.rda ├── dloop.g.rda ├── dolph.haps.rda ├── dolph.msats.rda ├── dolph.seqs.rda ├── dolph.strata.rda └── msats.g.rda ├── inst ├── CITATION ├── extdata │ └── dolph.seqs.fasta └── fastsimcoal2.html ├── man ├── LDgenepop.Rd ├── TiTvRatio.Rd ├── alleleFreqs.Rd ├── alleleSplit.Rd ├── allelicRichness.Rd ├── arlequin.Rd ├── as.data.frame.gtypes.Rd ├── as.multidna.Rd ├── baseFreqs.Rd ├── bowhead.snp.position.Rd ├── bowhead.snps.Rd ├── clumpp.Rd ├── createConsensus.Rd ├── df2gtypes.Rd ├── diagnosability.Rd ├── dloop.g.Rd ├── dolph.haps.Rd ├── dolph.msats.Rd ├── dolph.seqs.Rd ├── dolph.strata.Rd ├── dupGenotypes.Rd ├── evanno.Rd ├── expandHaplotypes.Rd ├── fasta.Rd ├── fixedDifferences.Rd ├── fixedSites.Rd ├── freq2GenData.Rd ├── fsc.input.Rd ├── fscRead.Rd ├── fscRun.Rd ├── fscWrite.Rd ├── fusFs.Rd ├── gelato.Rd ├── genepop.Rd ├── gtypes-class.Rd ├── gtypes.accessors.Rd ├── gtypes2genind.Rd ├── gtypes2genlight.Rd ├── gtypes2loci.Rd ├── gtypes2phyDat.Rd ├── gtypes2rfDF.Rd ├── gtypesRF.Rd ├── heterozygosity.Rd ├── hweTest.Rd ├── initialize-gtypes-method.Rd ├── is.gtypes.Rd ├── iupac.Rd ├── jackHWE.Rd ├── labelHaplotypes.Rd ├── landscape2gtypes.Rd ├── ldNe.Rd ├── lowFreqSubs.Rd ├── mRatio.Rd ├── maf.Rd ├── mafft.Rd ├── maverickRun.Rd ├── mega.Rd ├── microhaplot2rubias.Rd ├── mostDistantSequences.Rd ├── mostRepresentativeSequences.Rd ├── msats.g.Rd ├── neiDa.Rd ├── nucleotideDivergence.Rd ├── nucleotideDiversity.Rd ├── numAlleles.Rd ├── numGenotyped.Rd ├── numMissing.Rd ├── permuteStrata.Rd ├── phase.Rd ├── popGenEqns.Rd ├── popStructTest.Rd ├── privateAlleles.Rd ├── propUniqueAlleles.Rd ├── qual2prob.Rd ├── readGenData.Rd ├── removeUnusedSequences.Rd ├── sequence2gtypes.Rd ├── sequenceLikelihoods.Rd ├── sequenceRF.Rd ├── sfs.Rd ├── sharedLoci.Rd ├── show-gtypes-method.Rd ├── simGammaHaps.Rd ├── strataG-package.Rd ├── strataSplit.Rd ├── stratify.Rd ├── structure.Rd ├── structurePlot.Rd ├── summarizeAll.Rd ├── summarizeInds.Rd ├── summarizeLoci.Rd ├── summarizeSeqs.Rd ├── summary-gtypes-method.Rd ├── tajimasD.Rd ├── theta.Rd ├── trimNs.Rd ├── variableSites.Rd ├── write.nexus.snapp.Rd ├── writeGtypes.Rd └── zygosity.Rd ├── src ├── Makevars ├── Makevars.win ├── RcppExports.cpp ├── RcppExports.o ├── calc_FstStats.cpp ├── calc_FstStats.o ├── calc_Phist.cpp ├── calc_Phist.o ├── misc_funcs.cpp ├── misc_funcs.o └── strataG.so ├── tests ├── testthat.R └── testthat │ ├── test-gtypes.accessors.R │ ├── test-gtypes.conversions.R │ ├── test-gtypes.creation.R │ ├── test-locus.summaries.R │ ├── test-popStructStats.R │ ├── test-private.alleles.R │ ├── test-sequence.summaries.R │ ├── test-shared.loci.R │ └── validation_results.rdata └── vignettes ├── external.programs.Rmd ├── external.programs.html ├── gtypes.R ├── gtypes.Rmd ├── gtypes.html ├── msats.csv ├── sequences.R ├── sequences.Rmd ├── sequences.html ├── summaries.R ├── summaries.Rmd └── summaries.html /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EricArcher/strataG/HEAD/.Rbuildignore 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