DNA.dist {QSutils} | R Documentation

## 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

[Package QSutils version 1.2.0 Index]