Finding sites with variation

Source: R/SNPsites.R

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.

SNPsites(tree, ...)

# S3 method for 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)
#> This is a 'SNPsites' object. 
#> 
#> 106 123 139 196 784 894 988 1542 2074 2086 2634 2787 3045 3162