msa.tree {EnvNJ} R Documentation

## Infer a tree based on a MSA

### Description

Infers a tree base on a MSA.

### Usage

msa.tree(data, outgroup = 'any')


### Arguments

 data input data must be a dataframe where each row corresponds to a protein and each column to a species. outgroup when a rooted tree is desired, indicate the species to be used as outgroup.

### Details

The input data has the same format that the input data used for EnvNJ or SVD-n-Gram methods. Thus, the name of columns must correspond to that of species.

### Value

A list containing the (i) MSA, (ii) the distance matrix and (iii) the tree.

## Not run: