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="USER") # for binary data
> all.trees<-allTrees(n=length(data),tip.label=names(data),rooted=FALSE)
> pscores<-vector()
> for(i in 1:length(all.trees))
pscores[i]<-parsimony(all.trees[[i]],data)
> minscore<-min(pscores); mp.tree<-all.trees[pscores==minscore]
mp.tree will be a single MP tree or a list if there are several MP trees.
Of course this will take a long time for more than a 7 or 8 species, and
will not work at all for more than 10 species. It's also possible that
an exhaustive search in a traditional phylogeny inference program like
PAUP* might be faster if, for instance, PAUP* retains the score for
parts of the tree that don't change among a set of trees - instead of
recalculating it each time anew. That I don't know.
- Liam
--
Liam J. Revell
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://phytools.blogspot.com
On 3/28/2011 10:58 AM, Ross Mounce wrote:
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 analyses with it's lack of parallelisation.
Have you considered using TNT? http://www.cladistics.com/aboutTNT.html
Wiki Manual here: http://tnt.insectmuseum.org/index.php/Main_Page
Many paleontologists are starting to use this - computationally it's far more
efficient.
Just remember, as with any and all phylogenetic analyses it's "garbage in, garbage
out": you must know what you're doing and why *before* you start your analysis.
Kind Regards and good luck,
Ross Mounce
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