Okay, here is an example of what has me scratching my head. In the tree below, the software suggests that split #2 is essentially a lock. Split #4 also has strong evidence. But split 3 isn't in the same league.
So, if you were explaining the meaning of this to someone not schooled in trees, what is the best way to do it? Is it that we can't rule out that alternative topologies that lump E with F (sketched below) or E with G are not yet excluded from the data?
That's what I think this means, but the nagging issue is that the cladogram visual is a bit at odds with this -- visually it looks like F & G going together is a slam dunk. But then that confidence value wouldn't make much sense -- F & G are always going to be split from each other! Is it correct to say that 99.6% of trees have F & G as nearest neighbors? If that were the case, then how does E fit into the puzzle.
I suppose in the end what is messing with me is the sandwiching of a poor value between two really good ones. If 99.6% of trees have FG as a group and 100% have EFG as a group, then how can 16.5% of them not have E separate from FG?
So, who is up to schooling me?
UPDATE: Based on comment from Roy below, then most of the alternative topologies probably look like this rather than the second picture above, correct?
For the record, the maximum likelihood values were generated by FastTree and the tree displayed with Dendroscope, from which I screen-captured and then scribbled on with Microsoft's Snipping Tool.
I think I'm still muddled on splits vs. branches -- in my head the only way to identify a branch is by the set of data it splits off. But I think this is progress.