Matthew-
In addition to Ross's suggestion of TNT, I would recommend that you consider
options less commonly used by paleontologists. One option is Mr. Bayes,
which can apply the Mk2 model from Lewis (2001) to morphological data.
Another is Strataphy (Marcot and Fox, 2008) which can apply
Dear all,
I have been trying to get estimates of transition rates among
character states using fitDiscrete in geiger but it returns the
following error message:
fitDiscrete(tree, h1, model=ARD)
Warning: some tree transformations in GEIGER might not be sensible
for nonultrametric trees.
Matthew.
The only thing that I would add is that if you *really* want to do an
exhaustive search in R, and your species number is small enough to
permit an exhaustive search (i.e., =10), then it is straightforward
enough to do so:
require(phangorn)
Thanks Liam,
I have two small additions, the first on speeds things up but costs
memory, the second one just simplifies things a bit (and is maybe also
a bit faster).
Regards,
Klaus
On 3/28/11, Liam J. Revell liam.rev...@umb.edu wrote:
Matthew.
The only thing that I would add is that if you
Regarding finding all most parsimonious trees by branch-and-bound:
Program Penny in my PHYLIP package could be called from within R,
driven by batch scripts. You'd have to make them yourself, but it's
not hard. However Penny can handle only 0/1 characters, and if there
is a multifurcation it
