Question: Advice on publishing maximum likelihood trees
gravatar for weedy23
5 weeks ago by
weedy2330 wrote:

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!

ADD COMMENTlink written 5 weeks ago by weedy2330
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1649 users visited in the last hour