Same name on one tree (2 copies), add links to another tree problem

[jianshu93]

Hello ggtree team,

I have a special case for co-phylogeny (add links between 2 trees): I have 2 copies of the same gene with some divergency for the gene tree, a genome tree and I want to map gene tree to genome tree by name, so 2 genes will map to the same genome in the genome tree. Now by default, links were added within the first tree but not between 2 trees (see attached pdf format tree). Seems to be a bug to me or there is some parameter settings that I do not know. I attached 2 trees. I followed the example usage here: https://arftrhmn.net/how-to-make-cophylogeny/

Let me know how I can do it.

Many thanks!

Jianshu

tree_co-phylogeny.pdf

narG_OMZ_SAR11_aligned_new.tre.zip
OMZ_SAG_SAR11_gottree_new.tre.zip