This R package provides an interface to the C++ library NCL. It can parse efficiently common file formats used to store phylogenetic trees, especially NEXUS and Newick files.
This package is primarily intended to be used by package developers as it
extracts the elements needed to build R objects that represent the content of
the file. For instance, phylobase
uses rncl to extract trees and/or data stored in NEXUS and Newick files to
create objects of class phylo4 or phylo4d.
The package however provides two functions for users: read_nexus_phylo() and
read_newick_phylo(). They read NEXUS and Newick files respectively, and return
(a valid) phylo or multiPhylo object from the package
ape. These functions differ from those
found in ape (respectively read.tree and read.nexus) as rncl functions can
read trees with singletons, and missing branch lengths. However, rncl adheres
to the NEXUS standards and only accepts tip labels without white spaces and tip
labels cannot be duplicated in the same tree.