| calculatePi | Calculate population frequency at each SNP |
| computeReference | Compute the number of reference reads over a matrix |
| errorHet | Average absolute difference between expected heterozygosity |
| Expected_Het | Compute expected heterozygosity within a population |
| ExpHet_site | Compute expected heterozygosity per site |
| filterMinor | Filter sites according to a minor-allele reads threshold |
| filterPool | Filter Pool-seq data according to a minor-allele reads... |
| findMinor | Define major and minor alleles |
| forcePool | Randomly select the required number of loci from the pooled... |
| GetGenotypes | Create genotypes from a output with haplotypes |
| getNumReadsR_vector | Compute the number of reference reads |
| hap2geno | Convert haplotypes to genotypes |
| haplo.fix | Create invariable sites |
| Ifreqs | Compute allele frequencies from genotypes |
| indProbs | Probability of contribution of each individual |
| indReads | Reads contributed by each individual |
| maeFreqs | Average absolute difference between allele frequencies... |
| maeHet | Average absolute difference between the expected... |
| maePool | Average absolute difference between allele frequencies |
| mymae | Average absolute difference between allele frequencies... |
| numberReference | Compute the number of reference reads at multiple loci |
| numberReferencePop | Compute the number of reference reads for multiple... |
| Pfreqs | Compute allele frequencies from pooled sequencing data |
| 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... |
| popsReads | Simulate total number of reads for multiple populations |
| remove_by_reads | Apply a coverage-based filter over a list |
| remove_by_reads_matrix | Apply a coverage-based filter to a matrix |
| removeSites | Apply a minor allele reads threshold |
| 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 |
| splitMatrix | Split matrix of genotypes |
| strg2sync | Create sync string for a single SNP |
| strg2vcf | Create vcf string for a single SNP |
| vcfinfo | Create vcf table with relevant information |
| vcfloci | Create vcf string for all SNPs in multiple loci |
| vcflocus | Create vcf string for all SNPs in a single locus |
