Hi Matthew.
Just for fun, I tried to create a function that would do exhaustive and
branch & bound searches for the MP tree. I think I have done so
correctly. The link to the function is here:
http://anolis.oeb.harvard.edu/~liam/R-phylogenetics/exhaustiveMP/v0.1/exhaustiveMP.R
[Note this function is *very* slow for more than 7 or 8 tips.]
An example execution would be:
> source("exhaustiveMP.R") # load from source
> mp.trees<-exhaustiveMP(data) # which will do B&B
or
> mp.trees<-exhaustiveMP(data,method="exhaustive")
for instance.
- 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 4/1/2011 11:02 PM, Matthew Vavrek wrote:
Hello again all,
I got a number of great solutions to my last question about branch and
bound maximum parsimony searches, several of which had definitely not
crossed my mind. However, being stubborn (or is that stupid? Hard to
tell sometimes) I went ahead and have started putting together a branch
and bound style search function for R, just because (I'll try to get it
up on CRAN shortly). It works, however it's not as efficient as I think
it probably could be, probably because the method I use to add new taxa
to the tree involves text searches with grep to create Newick trees. All
that being said, is there any way to take an existing tree (in any
format, such as Newick, but also the edge lists like in an ape 'phylo'
object) and add a taxon at all the possible positions? I know allTrees()
exists, but that would give me all the possibilities, rather than a
restricted set (as I would need for branch and bound).
Thanks again
Matthew
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