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A B C D E F G H I J L M N O P R S T V W
| strataG-package | Summaries and population structure analyses of haplotypic and genotypic data |
| align.clustal | CLUSTAL Alignment |
| align.folder | Align Sequences in a Folder |
| align.mafft | MAFFT Alignment |
| allele.freq.format | Compiles and Formats Allele Frequencies |
| allele.freqs | Allele Frequencies |
| allele.split | Split Alleles For Diploid Data |
| allelic.richness | Allelic Richness |
| arlequin | Read and Write Arlequin Files |
| as.data.frame.gtypes | Coerce to a Data Frame |
| as.dna.seq | Format List of DNA Sequences |
| as.matrix.gtypes | Coerce to a Matrix |
| base.freqs | Base Frequencies |
| bowhead.snp.position | Bowhead Whale SNP Genotype Groups |
| bowhead.snps | Bowhead Whale SNP Genotypes |
| check.genotypes | Run All Genotype QA/QC Tests |
| check.gtypes | Create a gtypes object |
| check.seqs | Run All Sequence QA/QC Tests |
| clumpp | Run CLUMPP |
| clumpp.run | Run CLUMPP |
| create.consensus | Consensus Sequence |
| Da | Nei's Da |
| decode | Decode 'gtypes' |
| decode.loci | Decode 'gtypes' |
| decode.sequences | Decode 'gtypes' |
| decode.strata | Decode 'gtypes' |
| diversity | Unbiased Estimate of Diversity |
| dolph.haps | Dolphin mtDNA Haplotype Sequences |
| dolph.msats | Dolphin Microsatellite Genotypes |
| dolph.seqs | Dolphin mtDNA Sequences |
| dolph.strata | Dolphin Genetic Stratification and Haplotypes |
| dup.genotypes | Duplicate Genotypes |
| exptd.het | Expected Heterozygosity |
| fasta | Read and Write FASTA |
| fastsimcoal | Run FASTSIMCOAL |
| fastsimcoal.run | Run FASTSIMCOAL |
| fastsimcoal.write | Run FASTSIMCOAL |
| fisher.method.p | Fisher's Method p-value |
| fixed.differences | Fixed Differences |
| fixed.sites | Fixed Sites |
| fst.to.nm | Nm from Fst |
| gelato | GELATo - Group ExcLusion and Assignment Test |
| gelato.plot | Plot GELATo |
| gelato.run | GELATo - Group ExcLusion and Assignment Test |
| gen.data.from.freq | Convert Haplotype Frequency Matrices |
| genepop | Run GENEPOP |
| genepop.run | Run GENEPOP |
| genepop.write | Run GENEPOP |
| gtype.struct.func | Population Structure Statistic Functions |
| gtype.struct.stat | Population Structure Statistic Functions |
| gtypes | Create a gtypes object |
| gtypes.character | Create a gtypes object |
| gtypes.default | Create a gtypes object |
| gtypes.list | Create a gtypes object |
| h.stats | Estimate Fixation Indices |
| hap.freqs | Haplotype Frequencies |
| haplotype.likelihoods | Haplotype Likelihoods |
| haplotypic.diversity | Haplotypic Diversity |
| hwe | Hardy-Weinberg Equilibrium |
| hwe.genepop | Hardy-Weinberg Equilibrium |
| is.aligned.seq | Format List of DNA Sequences |
| is.diploid | Check Ploidy |
| is.dna.seq | Format List of DNA Sequences |
| is.gtype.struct.func | Check Population Structure Function |
| is.gtypes | Create a gtypes object |
| is.haploid | Check Ploidy |
| is.ti.tv | Transition / Transversion Ratio |
| iupac.code | IUPAC Code |
| jack.hwe | Hardy-Weinberg Equlibrium Jackknife |
| jack.influential | Hardy-Weinberg Equlibrium Jackknife |
| jmodeltest.run | jModelTest |
| label.haplotypes | Find and label haplotypes |
| label.haplotypes.default | Find and label haplotypes |
| label.haplotypes.gtypes | Find and label haplotypes |
| linkage.genepop | Linkage Disequlibrium |
| locus.cols | Locus Information |
| locus.names | Locus Information |
| low.freq.subs | Low Frequency Substitutions |
| mega | Read and Write MEGA |
| merge.gtypes | Merge gtypes |
| most.distant.sequences | Most Distant Sequences |
| na.omit.gtypes | Omit Missing Data |
| nei.Da | Nei's Da |
| nucleotide.divergence | Nucleotide Divergence |
| nucleotide.diversity | Nucleotide Diversity |
| num.alleles | Number of Alleles |
| num.alleles.shared | Number of Shared Alleles |
| num.gens.eq | Number of Generations to Equilibrium |
| num.loci | Locus Information |
| num.missing | Number Missing Data |
| obsvd.het | Observed Heterozygosity |
| overall.test | Population Differentiation Tests |
| p.val | Permutation Test P-value |
| pairwise.shared.loci | Calculate Pairwise Shared Loci |
| pairwise.test | Population Differentiation Tests |
| pct.unique.haplotypes | Percent Unique Haplotypes |
| phase | PHASE |
| phase.filter | PHASE |
| phase.posterior | PHASE |
| phase.read.pair | PHASE |
| phase.read.sample | PHASE |
| phase.run | PHASE |
| phase.write | PHASE |
| plot.jack.influential | Hardy-Weinberg Equlibrium Jackknife |
| pop.diff.test | Population Differentiation Tests |
| print.gtypeSummary | Print gtypeSummary |
| read.arlequin | Read and Write Arlequin Files |
| read.fasta | Read and Write FASTA |
| read.gen.data | Read Genetic Data |
| read.mega | Read and Write MEGA |
| relabel.sequences | Relabel Sequences |
| restratify | Restratify gtypes |
| sequence.summary | Sequence Summary |
| shared.haps | Shared Haplotypes |
| sim.gamma.haps | Simulates Haplotypes |
| smry.by.locus | By-Locus Summaries |
| smry.by.sample | By-Sample Summaries |
| stat.chi2 | CHI-squared Analysis of Population Structure |
| stat.d.jost | Jost's D Estimate of Population Divergence |
| stat.fst | Fst Analysis of Population Structure |
| stat.fst.prime | F'st analysis of population structure |
| stat.gst | Gst Analysis of Population Structure |
| stat.gst.dbl.prime | G"st Analysis of Population Structure |
| stat.gst.prime.hedrick | Hedrick's G'st Analysis of Population Structure |
| stat.gst.prime.nei | Nei's G'st Analysis of Population Structure |
| stat.list | Population Differentiation Tests |
| stat.phist | PHIst Analysis of Population Structure |
| stopifnot.aligned | Format List of DNA Sequences |
| stopifnot.gtype.struct.func | Check gtype Population Structure Function |
| stopifnot.gtypes | Create a gtypes object |
| strata.pairs | Strata Pairs |
| strata.split | Split Strata |
| strataG | Summaries and population structure analyses of haplotypic and genotypic data |
| structure | STRUCTURE |
| structure.evanno | Run Evanno Method on STRUCTURE Results |
| structure.parse.q.mat | Parse Q-Matrix Text |
| structure.plot | Plot STRUCTURE Results |
| structure.read | STRUCTURE |
| structure.run | STRUCTURE |
| structure.write | STRUCTURE |
| subset.gtypes | Subset a gtypes Object |
| summarize.loci | Locus Summaries |
| summarize.sequences | DNA Sequence Summaries |
| summary.gtypes | Summarize gtypes Object |
| tajimas.d | Tajima's D |
| theta | Theta |
| ti.tv.ratio | Transition / Transversion Ratio |
| trim.ns | Trim N's From Sequences |
| valid.iupac.codes | Valid IUPAC Codes |
| variable.sites | Variable Sites |
| wright.fst | Wright's Fst |
| write.arlequin | Read and Write Arlequin Files |
| write.fasta | Read and Write FASTA |
| write.gtypes | write.gtypes |
| write.mega | Read and Write MEGA |
| write.snapp.nexus | Write NEXUS File for SNAPP |