Quasispecies Diversity

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Documentation for package ‘QSutils’ version 1.26.0

• 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