I want to compare two phylogenies and colour the association lines based on some metadata I have. I have been using ape cophyloplot but I have not had any success in getting the lines to colour accurately according to my data (see previous question).
Note that in my actual work flow I define the colour scheme using a palette to control the colour outcome.
I want a means to make a tangle using phylogenies which I can format. Preferably in R. I like to get an output like this: