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The functions are tailored for amplicon data     sets that have been filtered using the dada2 method (for more information on     dada2, visit <https://benjjneb.github.io/dada2/> ), but even other types of data     sets can be analyzed.    The ReplMatch() function matches replicates in data sets in order to evaluate     genotyping success.    The GetReplTable() and GetReplStats() functions perform such an evaluation.    The CreateFas() function creates a fasta file with all the sequences in the data     set.    The CreateSamplesFas() function creates individual fasta files for each sample in     the data set.    The DistCalc() function calculates Grantham, Sandberg, or p-distances from pairwise     comparisons of all sequences in a data set, and mean distances of all pairwise     comparisons within each sample in a data set. The function additionally outputs five     tables with physico-chemical z-descriptor values (based on Sandberg et al. 1998) for     each amino acid position in all sequences in the data set. These tables may be useful     for further downstream analyses, such as estimation of MHC supertypes.    The BootKmeans() function is a wrapper for the kmeans() function of the 'stats'    package, which allows for bootstrapping. Bootstrapping k-estimates may be    desirable in data sets, where e.g. BIC- vs. k-values do not produce clear    inflection points (\"elbows\"). BootKmeans() performs multiple runs of kmeans() and     estimates optimal k-values based on a user-defined threshold of BIC reduction. The     method is an automated and bootstrapped version of visually inspecting elbow plots     of BIC- vs. k-values.    The ClusterMatch() function is a tool for evaluating whether different k-means()     clustering models identify similar clusters, and summarize bootstrap model stats as     means for different estimated values of k. It is designed to take files produced by     the BootKmeans() function as input, but other data can be analysed if the     descriptions of the required data formats are observed carefully.    The PapaDiv() function compares parent pairs in the data set and calculate their     joint MHC diversity, taking into account sequence variants that occur in both     parents.    The HpltFind() function infers putative haplotypes from families in the data     set.     The GetHpltTable() and GetHpltStats() functions evaluate the accuracy of     the haplotype inference.    The CreateHpltOccTable() function creates a binary (logical) haplotype-sequence     occurrence matrix from the output of HpltFind(), for easy overview of which     sequences are present in which haplotypes.     The HpltMatch() function compares haplotypes to help identify overlapping and     potentially identical types.    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