Achaz.stats-methods     Achaz statistic
BayeScanR               An R implementation of BayeScan (Foll &
                        Gagiotti 2008)
F_ST.stats-methods      Fixation Index
F_ST.stats.2-methods    Fixation Index (2)
GENOME-class            Class "GENOME"
GFF_split_into_scaffolds
                        Split a GFF file into multiple scaffold-GFFs
MKT-methods             McDonald-Kreitman Test (McDonald & Kreitman
                        1991)
MS                      Coalescent simulation with or without selection
MS_getStats             Get the simulated MS/MSMS statistics
PG_plot.biallelic.matrix-methods
                        Plot the biallelic matrix
PopGenome               PopGenome
PopGplot                Smoothed line-plot for multiple populations
VCF_split_into_scaffolds
                        Split a VCF file into multiple scaffold-VCFs
Whop_readVCF            Reading tabixed VCF files (an interface to
                        WhopGenome)
calc.R2-methods         Linkage statistics (R2, P-value, Distance)
calc.fixed.shared-methods
                        Fixed and shared polymorphisms
codontable              Prints the codon table which is used in the
                        PopGenome framework
concatenate.classes     Concatenate GENOME classes
concatenate.regions     Concatenate regions
count.unknowns-methods
                        Calculate missing nucleotide frequencies
create.PopGenome.method
                        Integration of own functions into the
                        PopGenome-framework
detail.stats-methods    Several statistics
diversity.stats-methods
                        Diversities
diversity.stats.between-methods
                        Diversities
fasta_file              FASTA file (subdirectory "data")
get.biallelic.matrix-methods
                        Get the biallelic matrix
get.codons-methods      Detailed information about the nature of codon
                        changes
get.feature.names       Feature informations and GFF-attributes
get.individuals-methods
                        Print the names/IDs of individuals
get.status-methods      State of calculations
getBayes-methods        Get values for BayeScanR
get_gff_info            Annotation info
gff_file                GFF file (subdirectory "data")
introgression.stats-methods
                        Introgression statistics
jack.knife.transform,GENOME-method
                        Jacknife Transformation
linkage.stats-methods   Linkage Disequilibrium
load.session            Loading a PopGenome session
mult.linkage.stats-methods
                        Multilocus linkage statistics
neutrality.stats-methods
                        Neutrality Statistics
read.big.fasta          Reading large FASTA alignments
readData                Read alignments and calculate summary data
readHapMap              Read SNP data from the HapMap consortium
readMS                  Read output data from MS and MSMS
readSNP                 Read data in .SNP format
readVCF                 Read SNP data in tabixed VCF format
recomb.stats-methods    Recombination statistics
region.as.fasta-methods
                        Extract a region and write it to a FASTA file
save.session            Save the '"GENOME"' object of a PopGenome
                        session
set.filter-methods      Setting filter to the analysis
set.outgroup-methods    Define an outgroup
set.populations-methods
                        Define populations
set.ref.positions-methods
                        Set reference positions for SNP data
set.synnonsyn-methods   Set synonymous positions for SNP data
show.slots-methods      Show Slots of class GENOME
sliding.window.transform-methods
                        Sliding Window Transformation
snp_file                .SNP file (variant call data from 1001
                        Arabidopsis Genomes project)
split_data_into_GFF_attributes
                        Split the data into GFF attributes
split_data_into_GFF_features
                        Split the data into GFF features
splitting.data-methods
                        Split data into subsites
sweeps.stats-methods    Selective Sweeps
test.params-class       Set parameters for coalescent simulations with
                        Hudson's MS and Ewing's MSMS.
vcf_file                VCF file (subdirectory "data")
weighted.jackknife-methods
                        Weighted Jackknife
