read_tree: Read a newick formatted phylogenetic tree.

In cmmr/rbiom: Read/Write, Analyze, and Visualize 'BIOM' Data

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(src)

Arguments

src	Input data as either a file path, URL, or Newick string. Compressed (gzip or bzip2) files are also supported.

Value

A phylo class object representing the tree.

See Also

Other phylogeny: tree_subset()

Examples

    library(rbiom)
    
    infile <- system.file("extdata", "newick.tre", package = "rbiom")
    tree <- read_tree(infile)
    
    tree <- read_tree("
        (t9:0.99,((t5:0.87,t2:0.89):0.51,(((t10:0.16,(t7:0.83,t4:0.96)
        :0.94):0.69,(t6:0.92,(t3:0.62,t1:0.85):0.54):0.23):0.74,t8:0.1
        2):0.43):0.67);")

cmmr/rbiom documentation built on April 28, 2024, 6:38 a.m.