| allhap | Find all possible haplotypes | 
| allHaplotypes | get all haplotypes for the given markers | 
| build_ahccompletelist | generate a list with all haplotype combinations | 
| calcMrkHaptable | produce a table of nr of markers vs nr of haplotypes | 
| calcStatistics | calculate some statistics of the solutions of all haploblocks | 
| checkmrkDosage | check a marker dosages matrix or data.frame | 
| compareHapMrkDosages | compare haplotyping results with observed markers dosages | 
| compareHapresults | compare two haplotyping results | 
| demo_ped | pedigree | 
| demo_snpdos | dosages of SNP alleles | 
| expandHapdos | Add dropped rows back to haplotype dosage matrix | 
| getFSfreqs | get all FS haplotype combinations expected from two parental haplotype combinations, with their frequencies | 
| getGameteFreqs | get all gametes and their frequencies for a parental haplotype combination | 
| hapcomb2hapdos | convert haplotype combinations to haplotype dosages | 
| hapdos2hapcomb | convert haplotype dosages to haplotype combinations | 
| hapdos2mrkdos | calculate the marker dosages resulting from haplotype dosage combinations | 
| haploblock_df2list | convert a haploblock-defining data frame to a list | 
| inferHaplotypes | infer haplotypes for one or more haploblocks | 
| make.Happyinf.input | convert PolyHaplotyper input data to Happy-inf format | 
| make.SATlotyper.input | convert PolyHaplotyper marker data to SATlotyper format | 
| make.ShesisPlus.input | convert PolyHaplotyper marker data to ShesisPlus format | 
| mergeReplicates | merge replicate samples in dosage matrix | 
| mrkdid2mrkdos | get the marker dosages from mrkdids (marker dosage IDs) | 
| mrkdos2mrkdid | get marker dosage IDs from marker dosages | 
| overviewByFS | generate an overview of the results by haploblock and by FS family | 
| padded | pad an integer (prefix with zeroes to a fixed length) | 
| pedigreeHapCheck | check the consistency of haploblock genotypes over a pedigree | 
| pedigreeSim2PH | convert the PedigreeSim true haplotypes to marker dosages and haplotype dosages | 
| phblocks | List of markers per haploblock | 
| phdos | dosages of SNP alleles | 
| phFS | members of FS families | 
| phpar | parents of FS families | 
| phped | pedigree | 
| phresults | haplotyping results | 
| read.Happyinf.output | read the haplotyping results from the Happy-inf output | 
| read.SATlotyper.output | read the haplotyping results from the SATlotyper output | 
| read.ShesisPlus.output | Read the haplotyping results from the ShesisPlus output | 
| run.SATlotyper | A simple interface to run SATlotyper | 
| showOneFS | show marker and haplotype dosages for one FS family | 
| totHapcombCount | calculate the total nr of possible haplotype combinations | 
| usedhap | Find all used (inferred) haplotypes |