| 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'.
See Also
envnj(), fastaconc()
Examples
## Not run: env.fasta(file = "./data_t/sample5.fasta")