msa.tree: Infer a tree based on a MSA

In EnvNJ: Whole Genome Phylogenies Using Sequence Environments

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.

See Also

msa.merge

Examples

## Not run: 
data(bovids)
msa.tree(bovids)
## End(Not run)

EnvNJ documentation built on Sept. 27, 2021, 5:07 p.m.