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?
PAML is somewhat notorious for having a steep learning curve. You may try POTION or LMAP, which are supposedly easier wrappers around PAML. But my recommendation is to use ETE Toolkit 3, it makes it easy to automate PAML runs for several genes and it has some nice format manipulation and tree printing capabilities. See a short tutorial here.