Hi, I am relatively new to phylogenetic analyses so I have a simple question. I have done a multi-species maximum likelihood analysis in Garli. I have obtained a "best" tree in Garli from multiple runs. I then conducted a bootstrap analysis (1000 replicates) and imported the 1000 bootstrap trees into PAUP* to obtain a majority rule consensus tree.
My question is, which tree should I present in a publication? Are you supposed to present your "best" ML estimate tree and add the bootstrap values onto it, or the majority rule tree with bootstrap values itself? Most journal articles I've read do not make it clear what the tree is.
This makes a difference because my majority rule tree has lots of polytomies where the bootstrap support for certain clades is low so the trees are quite different.
Many thanks for helping out a newbie!