Man pages for strataG
Summaries and Population Structure Analyses of Genetic Data
| alleleFreqs | Allele Frequencies |
| alleleSplit | Split Alleles For Diploid Data |
| allelicRichness | Allelic Richness |
| arlequin | Read and Write Arlequin Files |
| as.data.frame.gtypes | Convert 'gtypes' to data.frame or matrix |
| as.multidna | Convert to multidna |
| baseFreqs | Base Frequencies |
| bowhead.snp.position | Bowhead Whale SNP Genotype Groups |
| bowhead.snps | Bowhead Whale SNP Genotypes |
| clumpp | Run CLUMPP |
| createConsensus | Consensus Sequence |
| df2gtypes | Convert a data.frame to gtypes |
| dloop.g | Dolphin dLoop gtypes Object |
| dolph.haps | Dolphin mtDNA Haplotype Sequences |
| dolph.msats | Dolphin Microsatellite Genotypes |
| dolph.seqs | Dolphin mtDNA D-loop Sequences |
| dolph.strata | Dolphin Genetic Stratification and Haplotypes |
| dupGenotypes | Duplicate Genotypes |
| evanno | Run Evanno Method on STRUCTURE Results |
| expandHaplotypes | Expand Haplotypes |
| fasta | Read and Write FASTA |
| fixedDifferences | Fixed Differences |
| fixedSites | Fixed Sites |
| freq2GenData | Convert Haplotype Frequency Matrices |
| fsc.input | Input functions for fastsimcoal parameters |
| fscRead | Read fastsimcoal output |
| fscRun | Run fastsimcoal |
| fscWrite | Write fastsimcoal2 input files |
| fusFs | Fu's Fs |
| gelato | GELATo - Group ExcLusion and Assignment Test |
| genepop | Run GENEPOP |
| gtypes2genind | Convert Between 'gtypes' And 'genind' objects. |
| gtypes2loci | Convert Between 'gtypes' And 'loci' objects. |
| gtypes2phyDat | Convert Between 'gtypes' And 'phyDat' objects. |
| gtypes.accessors | 'gtypes' Accessors |
| gtypes-class | 'gtypes' Class |
| gtypes.show | Show a gtypes object |
| heterozygosity | Heterozygosity |
| hweTest | Hardy-Weinberg Equilibrium |
| initialize-gtypes-method | 'gtypes' Constructor |
| is.gtypes | Test if object is 'gtypes' |
| iupac | IUPAC Codes |
| jackHWE | Hardy-Weinberg Equlibrium Jackknife |
| labelHaplotypes | Find and label haplotypes |
| landscape2gtypes | Convert Rmetasim landscape |
| LDgenepop | Linkage Disequlibrium |
| ldNe | ldNe |
| lowFreqSubs | Low Frequency Substitutions |
| maf | Minor Allele Frequencies |
| mafft | MAFFT Alignment |
| maverickRun | Run MavericK |
| mega | Read and Write MEGA |
| mostDistantSequences | Most Distant Sequences |
| mostRepresentativeSequences | Representative Sequences |
| mRatio | M ratio |
| msats.g | Dolphin Microsatellite gtypes Object |
| neiDa | Nei's Da |
| nucleotideDivergence | Nucleotide Divergence |
| nucleotideDiversity | Nucleotide Diversity |
| numAlleles | Number of Alleles |
| numGenotyped | Number of Individuals Genotyped |
| numMissing | Number Missing Data |
| permuteStrata | Permute strata |
| phase | PHASE |
| popGenEqns | Population Genetics Equations |
| popStructStat | Population structure statistics |
| popStructTest | Population Differentiation Tests |
| privateAlleles | Private Alleles |
| propUniqueAlleles | Proportion Unique Alleles |
| readGenData | Read Genetic Data |
| removeSequences | Remove Sequences |
| sequence2gtypes | Convert Sequences To 'gtypes' |
| sequenceLikelihoods | Sequence Likelihoods |
| sfs | Site Frequency Spectrum |
| sharedLoci | Shared Loci |
| simGammaHaps | Simulate Haplotypes |
| strataG-package | Summaries and population structure analyses of DNA sequence... |
| strataSplit | Split Strata |
| stratify | Stratify gtypes |
| structure | STRUCTURE |
| structurePlot | Plot STRUCTURE Results |
| summarizeAll | Summarize Genotypes and Sequences |
| summarizeInds | Individual Summaries |
| summarizeLoci | Locus Summaries |
| summarizeSeqs | Sequence Summaries |
| summary-gtypes-method | Summarize gtypes Object |
| tajimasD | Tajima's D |
| theta | Theta |
| TiTvRatio | Transition / Transversion Ratio |
| trimNs | Trim N's From Sequences |
| variableSites | Variable Sites |
| writeGtypes | Write 'gtypes' |
| write.nexus.snapp | Write NEXUS File for SNAPP |
