envnj: Build Trees Based on the Environment Around the Indicated...

In EnvNJ: Whole Genome Phylogenies Using Sequence Environments

Description

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

Usage

envnj(data, r = 10, aa = 'all', metric = "cosine", clustering = "nj", outgroup = 'any')

Arguments

data	input data must be a dataframe where each row corresponds to a protein sequence and each column to a species.
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.
metric	character string indicating the metric (see metrics() to see the methods allowed).
clustering	string indicating the clustering method, either "nj" or "upgma".
outgroup	when a rooted tree is desired, it indicates the species to be used as outgroup.

Details

This function builds alignment-independent phylogenetic trees.

Value

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

See Also

otu.space(), metrics()

Examples

data(bovids)
envnj(bovids[, 7:11], aa = "all", outgroup = "Pseudoryx_nghetinhensis")

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