Hi HyPhyers, I am using AnalyzeCodonData to examine dN dS patterns in several genes in a clade of fishes.  In the output, we have the list of results like this:

givenTree.Node82.nonSynRate=0
givenTree.SCARUS_SPINUS.synRate=9.51535
givenTree.Node82.synRate=4.43235
givenTree.Node56.synRate=3.27021
givenTree.Node56.nonSynRate=0
givenTree.SCARUS_SPINUS.nonSynRate=0

And then we have the E[Syn subs/nucleotide site] tree and the E[Non-syn subs/nucleotide site] tree:  and the dS and dN trees. 

Can you briefly tell me the differences between, for example SynRate at a node, Syn subs/nucleotide site branch lengths, and dS branch lengths?

I am also interested in how one would back calculate the actual number of S or N substitutions on a particular branch, and which would be best to use for dN/dS ratio. 

Finally, I cannot use the menu item dN/dS for branches no matter how complex the model I use- any idea why not?

Thank you, HyPhy is an excellent package.