I would like to calculate the dn/ds ratio for a series of genes for 5 different species. I am trying to use PAML, but I'm having a difficult time figuring out how to use it. I've look at Yang's manual (http://abacus.gene.ucl.ac.uk/software/pamlDOC.pdf) and other various tutorials, but the material is still over my head. I can't figure out how to get the multiple alignment sequence in the correct format and I don't understand what the treefile is all about, among other things. Does anyone have a detailed guide to using PAML for beginners?