print_annotated: Serialize an annotated phylogenetic tree

In phylotate: Phylogenies with Annotations

Description

This function takes the given tree object and returns a string representing the tree in the requested format. The difference between the "newick" and "newick.named" formats is that the former uses only node numbers in its output, whereas the latter uses the tip labels (sanitized and deduplicated if necessary).

Usage

print_annotated(tree, format="nexus")

Arguments

tree	a phylogentic tree, with optional annotations
format	a format specifier; either "nexus", "newick", or "newick.named"

Details

The tree object should be either a "phylo" or "multiPhylo" object. It may optionally be augmented with annotations, as described in the documentation for the parse_annotated function.

The output is a string suitable for writing to a file.

Value

a string containing a serialized tree.

Author(s)

Daniel Beer [e-mail]

See Also

parse_annotated, read_annotated, write_annotated

phylotate documentation built on June 30, 2019, 1:01 a.m.