SegSites {QSutils} | R Documentation

## Compute the number of segregating sites

### Description

Computes the number of segregating (polymorphic) sites in a given alignment. That is, the number of sites with more than a single nucleotide or amino acid in the alignment.

### Usage

    SegSites(seqs)

### Arguments

`seqs` | DNAStringSet or AAStringSet with the haplotype sequences.

### Value

A value corresponding to the number of polymorphic sites.

### Author(s)

Mercedes Guerrero-Murillo and Josep Gregori

### References

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

`ReadAmplSeqs`

### Examples

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

    SegSites(lst$hseqs)

[Package QSutils version 1.5.0 Index]