Hi Scott,
The reason for implementing only the consensus on the topology was after
reading the appropriate chapter in Inferring Phylogenies. So I'm glad
that Joe himself stepped in. I have added this reference in the help
page (it was already cited in my book with respect to this issue).
I
Emmanuel Paradis wrote:
If you are Bayesian, the trees sampled from an MCMC are here for estimation
including of the branch lengths, so you use them to compute some sort of
consensus topology as well as its branch lengths. So it makes sense that
MrBayes can do a consensus tree with branch
Dear Scott,
What should branch lengths on a consensus tree represent?
They cannot be expected substitutions per residue. This would imply no
evolution at points where uncertain branching patterns have been reduced
to a multi-furcation - which is not what the multi-furcation is meant to
imply.
I have a function to create a consensus tree with branch lengths. You feed
it a given topology (often a consensus topology, made with ape), then a
list of trees, and tell it what you want the branch lengths to represent.
It could be the proportion of input trees with that edge (good for
Dear Brian,
Awesome. Thanks for sharing the code Brian. I will give it a try. I see
what you all mean now more precisely with the question of what does it
really mean to have branch lengths on a consensus tree.
Thanks, Scott
On Wed, Nov 21, 2012 at 11:10 AM, Brian O'Meara bome...@utk.edu
Dear Joe,
Thanks for your feedback on this question. I will go read those pages you
mentioned.
Scott
On Wed, Nov 21, 2012 at 5:19 PM, Joe Felsenstein j...@gs.washington.eduwrote:
Daniel Barker wrote:
What should branch lengths on a consensus tree represent?
Scott Chamberlain had
