Hi all,
the package PHYLOCH from Christoph Heibl seems to do exactly what Joe
Felsenstein suggested, calling Penny from within R. The homepage is
http://www.christophheibl.de/Rpackages.html
Regards,
Klaus
On 3/28/11, Joe Felsenstein wrote:
>
> Regarding finding all most parsimonious trees by b
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 wi
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 wrote:
> Matthew.
>
> The only thing that I would add is that if you *really* want to
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)
> data<-read.phyDat(file=filename,type="
Dear Matthew,
Branch and Bound searching is often unneccessary, are you sure you need to do
this? With enough random addition sequences (relative to dataset size) you
*will* find all MPTs.
PAUP* despite being familiar to many of us and very fully-featured, is
definitely ungainly for modern an
