The confusion of starting topology

[zhangwenda0518]

Hello, author, I have a puzzle
I have constructed a species tree by using nuclear genes, so can this species tree be used as the document of the starting topology?

And, what is the source of the starting topology? Is it a root tree?

Thanks！

[crsl4]

yes, the species tree can be the starting tree, and it does not need to be rooted. The starting tree is only used to help the optimization process. It is not kept fixed in any way.