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| pegas-package | Population and Evolutionary Genetics Analysis System |
| all.equal.haploNet | Compare Two Haplotype Networks |
| alleles2loci | Build Loci Object From Matrix of Alleles |
| amova | Analysis of Molecular Variance |
| as.igraph.haploNet | Haplotype Networks |
| as.loci | Conversion Among Allelic Data Classes |
| as.loci.character | Conversion Among Allelic Data Classes |
| as.loci.data.frame | Conversion Among Allelic Data Classes |
| as.loci.factor | Conversion Among Allelic Data Classes |
| as.loci.genind | Conversion Among Allelic Data Classes |
| as.network.haploNet | Haplotype Networks |
| bind.loci | Bind Loci Objects |
| cbind.loci | Bind Loci Objects |
| diffHaplo | Comparison Between Two Haplotypes |
| dist.hamming | Hamming Distance |
| dist.haplotype.loci | Haplotype Extraction and Frequencies From Allelic Data |
| edit.loci | Edit Allelic Data with R's Data Editor |
| expand.genotype | Utily Functions for pegas |
| Fst | F-Statistics |
| genind2loci | Conversion Among Allelic Data Classes |
| geod | Geodesic Distances |
| geoTrans | Manipulate Geographic Coordinates |
| getAlleles | Utily Functions for pegas |
| getGenotypes | Utily Functions for pegas |
| getINFO | Information From VCF Files |
| getPloidy | Utily Functions for pegas |
| H | Heterozygosity at a Locus Using Gene Frequencies |
| haploFreq | Haplotype Frequencies With a Covariate |
| haploNet | Haplotype Networks |
| haplotype | Haplotype Extraction and Frequencies |
| haplotype.character | Haplotype Extraction and Frequencies |
| haplotype.DNAbin | Haplotype Extraction and Frequencies |
| haplotype.loci | Haplotype Extraction and Frequencies From Allelic Data |
| heterozygosity | Heterozygosity at a Locus Using Gene Frequencies |
| hw.test | Test of Hardy-Weinberg Equilibrium |
| hw.test.genind | Test of Hardy-Weinberg Equilibrium |
| hw.test.loci | Test of Hardy-Weinberg Equilibrium |
| is.phased | Utily Functions for pegas |
| is.snp | Utily Functions for pegas |
| is.snp.VCFinfo | Information From VCF Files |
| jaguar | Jaguar Micro-Satellites |
| LD | Linkage Disequilibrium |
| LD2 | Linkage Disequilibrium |
| LDmap | Multi-Locus Linkage Disequilibrium |
| LDscan | Multi-Locus Linkage Disequilibrium |
| loci | Read Allelic Data Files |
| loci2genind | Conversion Among Allelic Data Classes |
| mjn | Median-Joining Network |
| MMD | Mismatch Distribution |
| msn | Minimum Spanning Tree and Network |
| mst | Minimum Spanning Tree and Network |
| na.omit.loci | Missing Allelic Data |
| nuc.div | Nucleotide Diversity |
| nuc.div.DNAbin | Nucleotide Diversity |
| nuc.div.haplotype | Nucleotide Diversity |
| pegas | Population and Evolutionary Genetics Analysis System |
| plot.haploNet | Haplotype Networks |
| plot.haplotype | Haplotype Extraction and Frequencies |
| plot.haplotype.loci | Haplotype Extraction and Frequencies From Allelic Data |
| plot.spectrum | Site Frequency Spectrum |
| plot.summary.loci | Print and Summaries of Loci Objects |
| plotNetMDS | Plot Networks With MDS Layout |
| print.amova | Analysis of Molecular Variance |
| print.haploNet | Haplotype Networks |
| print.haplotype | Haplotype Extraction and Frequencies |
| print.loci | Print and Summaries of Loci Objects |
| print.summary.loci | Print and Summaries of Loci Objects |
| print.VCFinfo | Information From VCF Files |
| proba.genotype | Utily Functions for pegas |
| R2.test | Ramos-Onsins-Rozas Test of Neutrality |
| rangePOS | Information From VCF Files |
| rbind.loci | Bind Loci Objects |
| read.gtx | Read Genetix Data Files |
| read.loci | Read Allelic Data Files |
| read.vcf | Read Variant Calling Format Files |
| replot | Edit the Layout of a Haplotype Network |
| rmst | Minimum Spanning Tree and Network |
| rr.test | Tajima Relative Rate Test of Molecular Clock |
| selectQUAL | Information From VCF Files |
| site.spectrum | Site Frequency Spectrum |
| sort.haplotype | Haplotype Extraction and Frequencies |
| subset.haplotype | Subsetting and Filtering Haplotypes |
| summary.loci | Print and Summaries of Loci Objects |
| tajima.test | Test of the Neutral Mutation Hypothesis |
| theta.h | Population Parameter THETA using Homozygosity |
| theta.k | Population Parameter THETA using Expected Number of Alleles |
| theta.msat | Population Parameter THETA From Micro-Satellites |
| theta.s | Population Parameter THETA using Segregating Sites |
| theta.s.default | Population Parameter THETA using Segregating Sites |
| theta.s.DNAbin | Population Parameter THETA using Segregating Sites |
| theta.tree | Population Parameter THETA Using Genealogy |
| VCFheader | Information From VCF Files |
| VCFlabels | Information From VCF Files |
| VCFloci | Information From VCF Files |
| write.loci | Write Allelic Data Files |
| [.haplotype | Haplotype Extraction and Frequencies |
| [.loci | Print and Summaries of Loci Objects |