rnaimehaom / rncl

An R interface to the Nexus Class Library (C++) to read in quickly large phylogenetic trees and data

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.

Development versions for Windows

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.