Man pages for pegas
Population and Evolutionary Genetics Analysis System
| alleles2loci | Build Loci Object From Matrix of Alleles |
| allelicrichness | Allelic Richness and Rarefaction Plots |
| all.equal.haploNet | Compare Two Haplotype Networks |
| amova | Analysis of Molecular Variance |
| bind.loci | Bind Loci Objects |
| by.loci | Summary by Population or Other Factor |
| conversion | Conversion Among Allelic Data Classes |
| cophenetic.haploNet | Cophenetic Matrix on Haplotype Networks |
| diffHaplo | Comparison Between Two Haplotypes |
| dist.asd | Allelic Sharing Distance |
| dist.hamming | Hamming Distance |
| edit.loci | Edit Allelic Data with R's Data Editor |
| F234 | F-Statistics From Patterson et al |
| Fst | F-Statistics |
| geod | Geodesic Distances |
| geoTrans | Manipulate Geographical Coordinates |
| hap.div | Haplotype Diversity |
| haploFreq | Haplotype Frequencies With a Covariate |
| haploNet | Haplotype Networks |
| haplotype | 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 |
| jaguar | Jaguar Micro-Satellites |
| LD | Linkage Disequilibrium |
| LDscan | Multi-Locus Linkage Disequilibrium |
| mjn | Median-Joining Network |
| MMD | Mismatch Distribution |
| mst | Minimum Spanning Tree and Network |
| mutations | Plot Mutations on Networks |
| na.omit.loci | Missing Allelic Data |
| nuc.div | Nucleotide Diversity |
| options_themes_haploNet | Options to Plot haploNet Objects |
| pegas-package | Population and Evolutionary Genetics Analysis System |
| plotNetMDS | Plot Networks With MDS Layout |
| R2.test | Ramos-Onsins-Rozas Test of Neutrality |
| 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 |
| rr.test | Tajima Relative Rate Test of Molecular Clock |
| site.spectrum | Site Frequency Spectrum |
| stairway | The Stairway Plot |
| subset.haplotype | Subsetting and Filtering Haplotypes |
| summary.loci | Print and Summaries of Loci Objects |
| sw | Sliding Windows |
| 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.tree | Population Parameter THETA Using Genealogy |
| utilities | Utily Functions for pegas |
| VCFloci | Information From VCF Files |
| write.loci | Write Allelic Data Files |
