Reads PANTHER db trees
The PANTHER Project handles a modified version of newick tree files which, besides of the tree structure, includes the type of node and ancestor labels. This function is a wrapper of ape::read.tree().
read_panther(x, tree.reader = ape::read.tree, ...) read.panther(x, tree.reader = ape::read.tree, ...)
x: Character scalar. Full path to the panther file.tree.reader: Function that will be used to read the tree file. It can be either ape::read.tree or rncl::read_newick_phylo....: Further arguments passed to ape::read.tree().A list consisting of a data.frame and a phylo object. The data.frame has the following columns:
branch_length: Numeric vector. Length of the branch to its parent node.
type: Character vector. Can be either "S" (speciation), "D"
(duplication), or "T" (horizontal transfer).
ancestor: Character vector. Name of the ancestor.
The nodeids can be identified using the rownames.
path <- system.file("tree.tree", package="aphylo") read_panther(path)
Other reading: read_nhx(), read_pli()