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 <[email protected]> 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 - [email protected] > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at http://www.mail-archive.com/[email protected]/ _______________________________________________ R-sig-phylo mailing list - [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/[email protected]/
