[R-sig-phylo] Searching only ultrametric trees

Hi Everyone, I'm working on testing the effects of a likelihood reweighting algorithm that I think will improve the use of morphometrics in phylogenetic analyses. To do that, I need to do a bunch of tree searches using simulated data. I'm using a modified form of the tree search script in the

[R-sig-phylo] Using Phylogenetic Signal

Hi Everyone, I'm measuring phylogenetic signal in a morphometric dataset using Pagel's Lambda and Blomberg's K. I tend to think of both of these as continuous values, but in reviewing the literature I've noticed that most authors treat phylogenetic signal as either there or not. The way that

[R-sig-phylo] Brownian Evolution

Hi all, I've been investigating the use of Pagel's lambda and run into a problem comparing trees that have a low speciation rate and no extinction with trees that have a high speciation rate and lots of extinction. I'm comparing phylogenetic signal in two characters. In the first, I simulate

[R-sig-phylo] ML tree search using continuous characters

Hi everyone, I was wondering if anyone knows a good R function or package for doing a maximum likelihood search for a phylogenetic tree using continuous characters. I'm aware of Rcontml, but I'm looking for something that I can change and modify the individual steps in the search process