env.fasta {EnvNJ} R Documentation

## Build Trees Based on the Environment Around the Indicated Amino Acid(s)

### Description

Builds trees based on the environment around the indicated amino acid(s).

### Usage

env.fasta(file, r = 10, aa = 'all', out.file = 'any')


### Arguments

 file path to the single multispecies fasta file to be used as input. r a positive integer indicating the radius of the sequence segment considered as environment. aa the amino acid(s) to be used to encoded the species. out.file path and name of output file. Only if intermediate results data want to be saved (see details).

### Details

This function builds alignment-independent phylogenetic trees. The input data is a fasta file. When an out.file path is provided, the environment sequences of each species and the vector representing each species are saved in the path provided.

### Value

A list with two objects, the first one is an inter-species distance matrix. The second one is an object of class 'phylo'.

## Not run: env.fasta(file = "./data_t/sample5.fasta")