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| QSutils-package | Quasispecies Diversity |
| Collapse | Collapse reads into haplotypes and frequencies |
| ConsSeq | Consensus sequence given an alignment and frequencies |
| CorrectGapsAndNs | Function to correct an alignment with gaps and Ns |
| DBrule | Genotyping by the DB rule |
| Diverge | Generate a set of diverging haplotypes |
| DNA.dist | Matrix of DNA distances given an alignment |
| DottedAlignment | Align haplotypes into a dotted alignment |
| DSFT | Downsampling followed by fringe trimming |
| FAD | Functional attribute diversity |
| fn.ab | Vector of abundances with different methods |
| FreqMat | Matrix of nucleotide or amino acid frequencies in alignment by position |
| GenerateVars | Generate variants of a given haplotype |
| GenotypeStandards_A-H.fas | Genotype standards of hepatitis B virus |
| geom.series | Geometric series |
| GetInfProfile | Information content profile of an alignment |
| GetQSData | Read the aligned sequences, filter at minimum abundance, and sort the sequences |
| GetRandomSeq | Generate a random sequence |
| GiniSimpson | Functions to calculate the GiniSimpson index |
| GiniSimpsonMVUE | Functions to calculate the GiniSimpson index |
| GiniSimpsonVar | Functions to calculate the GiniSimpson index |
| HCq | Set of functions to compute the Havrda-Charvat estimator |
| HCqProfile | Set of functions to compute the Havrda-Charvat estimator |
| HCqVar | Set of functions to compute the Havrda-Charvat estimator |
| Hill | Hill numbers |
| HillProfile | Hill numbers |
| IntersectStrandHpls | Forward and reverse strand haplotype intersections |
| MutationFreq | Mutation frequency with respect to the dominant haplotype |
| MutationFreqVar | Mutation frequency with respect to the dominant haplotype |
| MutsTbl | Table of mutation frequencies by position |
| NormShannon | Set of functions to compute Shannon entropy |
| NormShannonVar | Set of functions to compute Shannon entropy |
| NucleotideDiversity | Nucleotide diversity |
| PolyDist | Fraction of substitutions by polymorphic site |
| QSutils | Quasispecies Diversity |
| Rao | Functions to compute Rao’s entropy |
| RaoPow | Functions to compute Rao’s entropy |
| RaoPowProfile | Functions to compute Rao’s entropy |
| RaoVar | Functions to compute Rao’s entropy |
| ReadAmplSeqs | Read a fasta file with haplotypes and frequencies |
| Recollapse | Collapse reads into haplotypes and frequencies |
| Renyi | Rényi profiles |
| RenyiProfile | Rényi profiles |
| ReportVariants | Report variants |
| SegSites | Compute the number of segregating sites |
| Shannon | Set of functions to compute Shannon entropy |
| ShannonVar | Set of functions to compute Shannon entropy |
| SortByMutations | Sort haplotypes by mutations and abundance |
| SummaryMuts | Distribution of nucleotides or amino acids in polymorphic sites |
| TotalMutations | Number of Mutations |
| Toy.GapsAndNs.fna | Fasta file with raw reads with gaps and Ns |
| ToyData_10_50_1000.fna | Fasta file with 10 haplotypes, 50 basepairs in size. |
| ToyData_FWReads.fna | Fasta file with forward reads |
| ToyData_RVReads.fna | Fasta file with reverse reads. |
| UniqueMutations | Number of unique mutations |
| Unknown-Genotype.fna | Fasta file with reads of unknown genotype |