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 1.8.4 Index]