SNPsites: Finding sites with variation

In sitePath: Detection of site fixation in molecular evolution

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)

Example output

Registered S3 method overwritten by 'treeio':
  method     from
  root.phylo ape 
[1]  139  894  988 2074 2086 2634 3045

sitePath documentation built on April 17, 2021, 6:05 p.m.