Dear all,
I am looking for a way to create a cloudogram (representing thousands of gene trees) where branches are coloured according to the clades to which the species belong, rather than using a single colour. Ideally, the backbone branches would remain grey. An example of the desired output can be found here.
I considered combining the densityTree function with plotSimmap, using a color code for each clade, but this approach did not work as expected.
Does anyone have experience or suggestions on how to achieve this?
Thank you in advance for your advice!
Best regards,
Nicolas