DNA.dist: Matrix of DNA distances given an alignment

In VHIRHepatiques/QSutils: Quasispecies Diversity

Matrix of DNA distances given an alignment

Description

Function to compute a matrix of pairwise distances from DNA sequences using a model of DNA evolution. It relies on the dist.dna() function in the APE package.

Usage

DNA.dist(seqs, model = "raw", gamma = FALSE, pairwise.deletion = FALSE)

Arguments

seqs	DNAStringSet object with the aligned haplotypes.
model	Evolutionary model to compute genetic distance by default "raw", but "N", "TS", "TV", "JC69", "K80", "F81", "K81", "F84", "BH87", "T92","TN93", "GG95", "logdet", "paralin", "indel", or "indelblock" can also be used.
gamma	Gamma parameter possibly used to apply a correction to the distances or FALSE (by default).
pairwise.deletion	A logical indicating whether to delete sites with missing data (gaps) in a pairwise manner. The default is to delete sites with at least one missing datum in all sequences.

Value

Object of class "dist" with pairwise distances.

Author(s)

Mercedes Guerrero-Murillo and Josep Gregori

References

Paradis E., Claude J. and Strimmer K., APE: analyses of phylogenetics and evolution in R language. Bioinformatics. 2004, 20, 289-290

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.

See Also

dist.dna

Examples

filepath<-system.file("extdata","ToyData_10_50_1000.fna", package="QSutils")
lst <- ReadAmplSeqs(filepath,type="DNA")

dst <- DNA.dist(lst$hseqs,model="N")
dst

VHIRHepatiques/QSutils documentation built on April 27, 2024, 10:29 p.m.