Build a tree from a distance matrix — build

Hierarchical methods give a rooted, ultrametric tree. NJ and BIONJ give an unrooted tree; give outgroup to root it. Negative branch lengths from NJ are set to zero.

Usage

build_tree(dist, method = "upgma", outgroup = NULL)

Arguments

dist: A dist object.
method: A method from tree_choices().
outgroup: Optional sample name(s) to root an NJ or BIONJ tree on.

Value

A cl_tree list with phylo (an ape tree), hclust (for hierarchical methods), method and rooted.

Examples

d <- clusnalyst_demo("binary")
tr <- build_tree(compute_distance(d), "upgma")