ghost-tree standalone now accepts different graft levels and it will also accept a phylogenetic tree (and not just aligned seqs) as a foundation. Yay! This pic is just for fun… no need to read it. Just showing different graft levels.
q2-ghost-tree works for different graft levels but it will not accept a phylogenetic tree. It keeps saying that it needs aligned seqs but I added this code to allow either aligned seqs or phylogenetic tree as a foundation file but it’s not working for me. I really want it to be able to accept one of these three types. I know that Jai suggested making another command that uses a tree as the foundation, but it seems like more work and maintenance… 2nd opinion? Thanks!