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