I made phylogenetic tree using FastTree of an alignment ~2000 protein sequences. I am willing to know how the topology support for the branches can be checked since bootstrap is not feasible here. I am also wondering how to simplify such huge tree and name the branches. Thank you.
Bootstrap is alway feasible. I bootstrapped an entire genome.
Build a consensus tree from all the genes.
Sub sample some trees and ask how many times each bifurcation in the global/consensus tree is supported by the subset of trees.
This is a bootstrapping approach.