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.
Because this package contains some C++ code, it can be tricky to
build if you are using Windows. Unless you need a feature only available
on GitHub, install rncl from CRAN.
Otherwise, you can obtain a binary version from here
(unless the AppVeyor badge on top is gray, in which case you can
download an older version or come back in a few minutes, or red meaning
the current version is broken and you need to get an older version).
Once in appveyor, look for the file named rncl_X.Y.Z.zip
where X.Y.Z represent the version number (e.g.,
rncl_0.4.0.zip). Then you can install this compiled version
of the package directly from R.