arklumpus/TreeNode: Version 1.5.3

TreeNode is a library for reading, writing and manipulating phylogenetic trees in C# and R. It can open and create files in the most common phylogenetic formats (i.e. Newick/New Hampshire and NEXUS) and adds support for two new formats, the Newick-with-Attributes and Binary format. The C# library also supports the NCBI ASN.1 format (text and binary).

The Newick-with-Attributes (NWKA) format is an extension of the Newick format which makes it possible to specify any number of arbitrary attributes to associate to each node in the tree. The NWKA format is backwards compatible with the Newick format (all Newick trees are valid NWKA trees, and NWKA trees produced by TreeNode are valid Newick trees). A full description of this format is available in this repository.

The Binary format makes it possible to read just one tree from a file, without having to parse the whole file. Note that the name refers to the way the data are stored in the file (as opposed to text-based formats) - multifurcating trees can be represented in this format without any issue. A full description of this format is also available in this repository.

The TreeNode R package can be used to read and write files in these two formats. The tree produced by this package have the same structure (and, thus, are compatible with) the popular phylogenetics package ape.

The TreeNode C# library, in addition to providing methods to read and write phylogenetic tree files, also includes methods to manipulate the resulting trees (e.g. to reroot the tree, compute a consensus tree, find the last common ancestor of a group, etc.).

TreeNode is released under the GPLv3 licence.