SNPsites: Finding sites with variation

In Takkoona/sitePath: Phylogeny-based sequence clustering with site polymorphism

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)

Takkoona/sitePath documentation built on Sept. 28, 2022, 1:24 a.m.