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
HCq                     Set of functions to compute the Havrda-Charvat
                        estimator
Hill                    Hill numbers
IntersectStrandHpls     Forward and reverse strand haplotype
                        intersections
MutationFreq            Mutation frequency with respect to the dominant
                        haplotype
MutsTbl                 Table of mutation frequencies by position
NucleotideDiversity     Nucleotide diversity
PolyDist                Fraction of substitutions by polymorphic site
QSutils-package         Quasispecies Diversity
Rao                     Functions to compute Rao’s entropy
ReadAmplSeqs            Read a fasta file with haplotypes and
                        frequencies
Renyi                   Rényi profiles
ReportVariants          Report variants
SegSites                Compute the number of segregating sites
Shannon                 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
