# Quasispecies Diversity

## Documentation for package ‘QSutils’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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