Phylogenies with Annotations

phylotate provides functions that allow you to read and write NEXUS and Newick trees containing annotations, including those produced by MrBayes.

It does this by extending ape's phylo object type with extra data members containing per-node annotation information. This information is stored in such a way that it can be manipulated easily and will survive most manipulations using standard ape functions (e.g. reorder, chronopl).

See the documentation for the parse_annotated function for more information on how annotations are stored internally.

The functions you probably want to use for most things are read_annotated and write_annotated.

  • phylotate-package
  • phylotate
Documentation reproduced from package phylotate, version 1.3, License: MIT + file LICENSE

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