Geiger has an interface to pathd8; it has the beginnings of interfaces to other programs, too, but I don't think they're finished yet.
Best, Brian _______________________________________ Brian O'Meara Associate Professor Dept. of Ecology & Evolutionary Biology U. of Tennessee, Knoxville http://www.brianomeara.info Postdoc collaborators wanted: http://nimbios.org/postdocs/ Calendar: http://www.brianomeara.info/calendars/omeara On Mon, Sep 21, 2015 at 11:30 AM, Franz Krah <f.k...@mailbox.org> wrote: > Hi Roger, > Fast Solution: use pathd8 or r8s or treePL. Not in R... pathd8 should be > the easiest one since you just need a ultrametric tree... 1 sec in parthd8 > > Cheers, Franz > > > > > > On 21.09.2015, at 16:21, Fabian Roger <fabian.ro...@marine.gu.se> wrote: > > > > hej everyone > > > > I have a large phylogeny based on 16S RNA OTU data (> 7000 OTUs). In > order to calculate some metrics of phylogenetic diversity I need to make > the tree ultrametric. I thought about using the chronos function from the > ape package in R. > > > > However I run into two problems: the main problem is that for the full > tree the function fails with the error "Error in nlminb(start.para, f, g, > control = opt.ctrl, lower = LOW, upper = UP) : NA/NaN gradient evaluation” > > > > I have seen several question regarding this error on the mailing list, > but I haven’t seen a solution. Could anybody help with that? Not that if I > run small subsets of the full tree, it works without problems! > > > > Also, I am concerned about runtime issues. A quick simulation suggests > that runtime roughly scales linearly with the number of OTUs and that 10 > 000 OTUs should run in below 1 h (although I only simulated trees up to 140 > OTUs…) if that’s true it wouldn’t be all that bad, but does anybody know or > has experience on if thats actually true? > > > > thanks a lot for your help! > > > > best > > > > Fabian > > _______________________________________________ > > R-sig-phylo mailing list - R-sig-phylo@r-project.org > > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > > Searchable archive at > http://www.mail-archive.com/r-sig-phylo@r-project.org/ > > _______________________________________________ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at > http://www.mail-archive.com/r-sig-phylo@r-project.org/ > [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
