phylotate (version 1.3)

print_annotated: Serialize an annotated phylogenetic tree

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"

Value

a string containing a serialized tree.

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.

See Also

parse_annotated, read_annotated, write_annotated