write_annotated {phylotate}

Write an annotated phylogenetic tree to a file

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

write_annotated(tree, filename, format="nexus")

Arguments

tree

a phylogentic tree, with optional annotations

filename

a file to write no

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.

Author(s)

Daniel Beer [e-mail]

See Also

parse_annotated, print_annotated, read_annotated