SNPsites {sitePath} | R Documentation

## Finding sites with variation

### Description

Single nucleotide polymorphism (SNP) in the whole package refers to variation of amino acid. `SNPsite` will try to find SNP in the multiple sequence alignment. A reference sequence and gap character may be specified to number the site.

### Usage

    SNPsites(tree, ...)

    ## S3 method for class 'phyMSAmatched'
    SNPsites(tree, minSNP = NULL, ...)

### Arguments

`tree` | A `phyMSAmatched` object.
`...` | Other arguments
`minSNP` | Minimum number of a mutation to be a SNP. The default is 10th of the total tree tips.

### Value

A `SNPsites` object.

### Examples

    data(zikv_tree_reduced)
    data(zikv_align_reduced)
    tree <- addMSA(zikv_tree_reduced, alignment = zikv_align_reduced)
    SNPsites(tree)

[Package sitePath version 1.6.6 Index]