I was wondering if there are any R packages or tools that can determine the evolutionary rates of species given their tree (with branch lengths) and an alignment file for a specific gene. I want to see if some species belonging to a clade are evolving more quickly than the ancestral clades. Is this possible? I know dN/dS ratios can determine evolutionary rate across the whole file and clade models can asses partitions, but is there a way to get the INDIVIDUAL species evolutionary rate so I can average it myself? Or can I assume that clade models in PAML do this automatically if I put my whole clade as the foreground?
I was thinking something like Pagel's test but that doesn't seem to take into account sequence files...
If you have any ideas or know of an R package/tool that can do this please advice me !
