envnj {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
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")