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