Alistair- How many multifurcations are there, with how many branches each? If the number of potentially resulting trees is too high, it may not be possible to store all the possible trees in memory.
If your tree is small, you might try allTrees(), which is the only ready to use function I know of which gives all possible trees, but only for tree with up to 10 tips. If you have a tree with more than 10 taxa but one or two small polytomies, you could remove the polytomies out with extract.clade(), find all their resolutions with allTrees(), stick their descendant tips back onto the polytomy with bind.tree() and then stick them back into the original tree with bind.tree(). It sounds crazy, but I've written code that sort of does this for my tree, so that I can weigh polytomy resolution by the fit of the solutions to a model of preservation potential in the fossil record. It would still require some programming, though, for you to get what you want. -Dave On Sat, Mar 12, 2011 at 7:32 AM, Alastair Potts <pott...@gmail.com> wrote: > Good day all, > I was wondering if there was any way to get multi2di to return trees with > all possible combinations when breaking up a polytomy to a dichotomous > branching tree? > > The reason why I ask is that PAUP is returning non-binary trees from some > analyses (e.g. a set of most parsimonious trees). The consensus function > requires binary trees, so I use the multi2di function to force these trees > to binary trees. However, as not all possible trees are returned, just one > possibility, I am getting more resolution in my topology that is actually > present in the PAUP strict consensus tree when I use the consensus function. > > I've looked at the multi2di function thinking I may be able to get it to > return all trees - but it is a problem beyond my meagre programming skills. > > Any help would be much appreciated! > > Cheers, > Alastair > -- > ----------------------------------------------------------------- > Alastair Potts > PhD candidate > Botany Department > University of Cape Town > alastair.po...@uct.ac.za or pott...@gmail.com > University Private Bag, Rondebosch 7700, South Africa > or > PO Box 115, Loxton 6985, South Africa > Cell: 082 491-7275 > > _______________________________________________ > R-sig-phylo mailing list > R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > -- David Bapst Dept of Geophysical Sciences University of Chicago 5734 S. Ellis Chicago, IL 60637 http://home.uchicago.edu/~dwbapst/ _______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
