Ifreqs                  Compute allele frequencies from genotypes
Pfreqs                  Compute allele frequencies from pooled
                        sequencing data
calculatePi             Calculate population frequency at each SNP
computeReference        Compute the number of reference reads over a
                        matrix
errorHet                Average absolute difference between expected
                        heterozygosity
findMinor               Define major and minor alleles
getNumReadsR_vector     Compute the number of reference reads
indProbs                Probability of contribution of each individual
indReads                Reads contributed by each individual
maeFreqs                Average absolute difference between allele
                        frequencies computed from genotypes and from
                        Pool-seq data
maeHet                  Average absolute difference between the
                        expected heterozygosity computed from genotypes
                        and from Pool-seq data
maePool                 Average absolute difference between allele
                        frequencies
mymae                   Average absolute difference between allele
                        frequencies computed from genotypes supplied by
                        the user and from Pool-seq data
numberReferencePop      Compute the number of reference reads for
                        multiple populations
pool2sync               Create 'synchronized' file from Pool-seq data
pool2vcf                Create VCF file from Pool-seq data
poolPops                Create Pooled DNA sequencing data for multiple
                        populations
poolProbs               Probability of contribution of each pool
poolReads               Reads contributed by each pool
popReads                Compute number of reads for each individual and
                        across all sites
popsReads               Simulate total number of reads for multiple
                        populations
removeSites             Apply a minor allele reads threshold
remove_by_reads         Apply a coverage-based filter over a list
remove_by_reads_matrix
                        Apply a coverage-based filter to a matrix
run_scrm                Simulate a single population
simPoolseq              Simulate Pool-seq data
simReads                Simulate coverage at a single locus
simulateCoverage        Simulate total number of reads per site
