similarityMatrix {sitePath}R Documentation

Similarity between sequences

Description

Get similarity between aligned sequences with gap ignored.

Usage

similarityMatrix(tree)

Arguments

tree

The return from addMSA function.

Value

A diagonal matrix of similarity between sequences.

Examples

data(zikv_tree)
data(zikv_align)
tree <- addMSA(zikv_tree, alignment = zikv_align)
simMatrix <- similarityMatrix(tree)

[Package sitePath version 1.10.0 Index]