I would like to create an annotated tree from the output (.nwk) of PhyloPhlAn 3 using GraPhlan.
I tried to annotate the internal nodes, but I can’t get it to work.
graphlan_annotate.py tree.newick annot.xml --annot annotation.txt && graphlan.py annot.xml tree.png
Then I realized that most of the data in graphlan-master/example/ is not newick or nexus, but a hierarchical plain text file. Do I need to manually create such a plain text file in addition to the annotation file to be able to annotate it with detailed clade local annotations? I would like to retain the branch length information, so I would like to use graphlan directly from the PhyloPhlAn 3 output (.nwk) if possible.