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| pegas-package | Population and Evolutionary Genetics Analysis System |
| amova | Analysis of Molecular Variance |
| as.loci | 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.loci.vector | Conversion Among Allelic Data Classes |
| expand.genotype | Utily Functions for pegas |
| Fst | F-Statistics |
| genind2loci | Conversion Among Allelic Data Classes |
| getAlleles | Utily Functions for pegas |
| getGenotypes | Utily Functions for pegas |
| getPloidy | Utily Functions for pegas |
| H | Heterozygosity at a Locus Using Gene Frequencies |
| haploNet | Haplotype Networks |
| haplotype | Haplotype Extraction and Frequencies |
| heterozygosity | Heterozygosity at a Locus Using Gene Frequencies |
| hw.test | Test of Hardy-Weinberg Equilibrium |
| loci2genind | Conversion Among Allelic Data Classes |
| MMD | Mismatch Distribution |
| nuc.div | Nucleotide Diversity |
| pegas | Population and Evolutionary Genetics Analysis System |
| plot.haploNet | Haplotype Networks |
| plot.haplotype | Haplotype Extraction and Frequencies |
| plot.spectrum | Site Frequency Spectrum |
| plot.summary.loci | Print and Summaries of Loci Objects |
| print.amova | Analysis of Molecular Variance |
| print.loci | Print and Summaries of Loci Objects |
| print.summary.loci | Print and Summaries of Loci Objects |
| R2.test | Ramos-Onsins-Rozas Test of Neutrality |
| read.gtx | Read Genetix Data Files |
| read.loci | Read Allelic Data Files |
| site.spectrum | Site Frequency Spectrum |
| 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.s | Population Parameter THETA using Segregating Sites |
| theta.tree | Population Parameter THETA Using Genealogy |
| write.loci | Write Allelic Data Files |
| [.loci | Print and Summaries of Loci Objects |