read_tree: Read a newick formatted phylogenetic tree.

In ecodive: Parallel and Memory-Efficient Ecological Diversity Metrics

Read a newick formatted phylogenetic tree.

Description

A phylogenetic tree is required for computing UniFrac distance matrices. You can load a tree from a file or by providing the tree string directly. This tree must be in Newick format, also known as parenthetic format and New Hampshire format.

Usage

read_tree(newick, underscores = FALSE)

Arguments

newick	Input data as either a file path, URL, or Newick string. Compressed (gzip or bzip2) files are also supported.
underscores	If TRUE, underscores in unquoted names will remain underscores. If FALSE, underscores in unquoted named will be converted to spaces.

Value

A phylo class object representing the tree.

Examples

    tree <- read_tree("
        (A:0.99,((B:0.87,C:0.89):0.51,(((D:0.16,(E:0.83,F:0.96)
        :0.94):0.69,(G:0.92,(H:0.62,I:0.85):0.54):0.23):0.74,J:0.1
        2):0.43):0.67);")
    class(tree)

ecodive documentation built on Aug. 23, 2025, 1:13 a.m.