I have three questions hoping to be clarified here.
First, I’d like to construct a combination of bacterial and archaeal tree of life using the 120 bacterial and 122 archaeal marker genes implemented in the tool and place my own MAGs on the tree. I figured that the .tree file produced from the de_novo_wf could serve this purpose, I am just trying to make sure if this is the right approach to go about what I am trying to achieve here.
In addition, it seems that the classify workflow is used for taxonomic classifications, while the de novo workflow is better from tree construction, but both workflows produce a tree file, what is the difference between the tree file produced from the two workflows?
Lastly, what does it mean to decorate a tree? Does it mean to assign taxonomy info into the tree? I would like to color the branches of the tree base on their corresponding phylum using ggtree, so is it possible to only assign phylum info onto the tree branches?
I appreciate any help you could provide, thank you!