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
