What is the best practice for gene tree - species tree reconcilation?

Question

[1099]

when you have a gene tree and you reconcile this with a species tree, how important is it to consider multiple forms of species trees? Does it suffice, to use (e.g.) NCBI species tree ? What is the best practice for reconcilation? I have used NOTUNG in analysis for reconcilation, but in this, user has to specify species tree and gene tree to reconcile, and that means you basically “limit” this reconcilation by choosing a specific form of species tree...