Re: [R-sig-phylo] Negative state probabilities with ace

Hi Dan, Thanks a lot for poiting precisely the problem with ace. The only problem with your fix is that the standard-error of the rates ($se) are on the transformed (log) scale and taking their exponential is not adequate. I modified ace() so that it now uses nlminb instead of nlm with bounds on

[R-sig-phylo] taxa order in plot.phylo

Hi, I have a cosmetic question. Is it possible to reverse the order with which taxa are plotted in plot.phylo? What I mean is this - in the following example, the taxa are plotted in top-to-bottom order Passeriformes to Struthioniformes. I'd like to have Struthioniformes at the top