An R interface to the NEXUS Class Library

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.