vect2tree: Convert a Set of Vectors into a Tree

In EnvNJ: Whole Genome Phylogenies Using Sequence Environments

Description

Converts a set of vectors into a tree.

Usage

vect2tree(path, metric = "cosine", clustering = "nj")

Arguments

path	path to the working directory. This directory must contain a txt file per vector and an additional txt file named vlist.txt that provides the names (one per line) of the vector txt files.
metric	character string indicating the metric (see metrics() to see the methods allowed).
clustering	string indicating the clustering method, either "nj" or "upgma".

Details

This function computes the distance matrix and builds the corresponding tree.

Value

a list with two elements: a distance matrix and a tree.

See Also

envnj(), fastaconc(), envfascpp()

Examples

## Not run: vec2tree("./data_t")

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