NucleotideDiversity: Nucleotide diversity
In QSutils: Quasispecies Diversity

Description Usage Arguments Value Author(s) References See Also Examples

Computes the mean pairwise genetic distance between sequences in the alignment.

1	NucleotideDiversity(dst,w=NULL)

`dst`	A "dist" object or a symmetrical matrix with haplotype pairwise distances (ie, the output of DNA.dist).
`w`	An optional numeric vector with the haplotype counts. When `w` is NULL, the same weight is given to each haplotype, and nucleotide diversity is computed at the entity level.

A value that corresponds to the nucleotide diversity, either by entity or abundance, depending on argument w.

Mercedes Guerrero-Murillo and Josep Gregori

Gregori J, Perales C, Rodriguez-Frias F, Esteban JI, Quer J, Domingo E. Viral quasispecies complexity measures. Virology. 2016 Jun;493:227-37. doi: 10.1016/j.virol.2016.03.017. Epub 2016 Apr 6. Review. PubMed PMID: 27060566.

Gregori J, Salicrú M, Domingo E, Sanchez A, Esteban JI, Rodríguez-Frías F, Quer J. Inference with viral quasispecies diversity indices: clonal and NGS approaches. Bioinformatics. 2014 Apr 15;30(8):1104-1111. Epub 2014 Jan 2. PubMed PMID: 24389655.

DNA.dist, ReadAmplSeqs

# Load haplotype alignment with abundances.
filepath<-system.file("extdata","ToyData_10_50_1000.fna", package="QSutils")
lst <- ReadAmplSeqs(filepath,type="DNA")

# Compute the DNA distance matrix. 
dst <- DNA.dist(lst$hseqs,model="K80")

NucleotideDiversity(dst, lst$nr) 
NucleotideDiversity(dst)