I have a biopython program that uses newick NHX extensions to pass information to the "R" tree plotting program ggtree. I am certain this used to work, but with the current version of biopython, it does not seem possible to write arbitrary comments in newick output.
(1) Am I confused, has BioPython phylo.write('newick') never supported NHX comments? (2) is there an option for phylo.write() to write out the comment string?