SNPsites: Finding sites with variation

Description Usage Arguments Value Examples

View source: R/SNPsites.R

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

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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

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wuaipinglab/sitePath documentation built on July 25, 2021, 9:11 p.m.