Man pages for QSutils
Quasispecies Diversity

CollapseCollapse reads into haplotypes and frequencies
ConsSeqConsensus sequence given an alignment and frequencies
CorrectGapsAndNsFunction to correct an alignment with gaps and Ns
DBruleGenotyping by the DB rule
DivergeGenerate a set of diverging haplotypes
DNA.distMatrix of DNA distances given an alignment
DottedAlignmentAlign haplotypes into a dotted alignment
DSFTDownsampling followed by fringe trimming
FADFunctional attribute diversity
fn.abVector of abundances with different methods
FreqMatMatrix of nucleotide or amino acid frequencies in alignment...
GenerateVarsGenerate variants of a given haplotype
GenotypeStandards_A-H.fasGenotype standards of hepatitis B virus
geom.seriesGeometric series
GetInfProfileInformation content profile of an alignment
GetQSDataRead the aligned sequences, filter at minimum abundance, and...
GetRandomSeqGenerate a random sequence
GiniSimpsonFunctions to calculate the GiniSimpson index
HCqSet of functions to compute the Havrda-Charvat estimator
HillHill numbers
IntersectStrandHplsForward and reverse strand haplotype intersections
MutationFreqMutation frequency with respect to the dominant haplotype
MutsTblTable of mutation frequencies by position
NucleotideDiversityNucleotide diversity
PolyDistFraction of substitutions by polymorphic site
QSutils-packageQuasispecies Diversity
RaoFunctions to compute Rao’s entropy
ReadAmplSeqsRead a fasta file with haplotypes and frequencies
RenyiRényi profiles
ReportVariantsReport variants
SegSitesCompute the number of segregating sites
ShannonSet of functions to compute Shannon entropy
SortByMutationsSort haplotypes by mutations and abundance
SummaryMutsDistribution of nucleotides or amino acids in polymorphic...
TotalMutationsNumber of Mutations
ToyData_10_50_1000.fnaFasta file with 10 haplotypes, 50 basepairs in size.
ToyData_FWReads.fnaFasta file with forward reads
ToyData_RVReads.fnaFasta file with reverse reads.
Toy.GapsAndNs.fnaFasta file with raw reads with gaps and Ns
UniqueMutationsNumber of unique mutations
Unknown-Genotype.fnaFasta file with reads of unknown genotype
QSutils documentation built on Nov. 1, 2018, 2:18 a.m.