[R-sig-phylo] Problems with dependency Biostrings

Hello all, there have been a few reports of problems with installing phytools or phangorn and you may see something like this: devtools::install_github("liamrevell/phytools") Downloading GitHub repo liamrevell/phytools@master Installing phytools Skipping 1 packages not available: Biostrings ...

[R-sig-phylo] interpreting PGLS results when lambda>1

Hi everyone, I have been running PGLS with gls from NLME and phyl.resid from PHYTOOLS. Most of my analyses are running well with no problems and give the same results in both packages. With just a few of my dependent variables, which happen to be evolutionary rates extracted from the program

[R-sig-phylo] Detecting homoplasy

Hi all, I am interested in finding homoplasious sites in a nucleotide sequence alignment on a ML tree calculated from that alignment. Is there a commonly used approach for doing this in ape, phangorn etc. I have tried a number of google searches based around 'R homoplasy' but cant find