What are the state of the art programs/libraries for performing dn/ds analyses? I know PAML can do it, but I'm wondering if there are others.
I usually work in C++, so I'm particularly interested interested in C++ libraries - does Seqan or the NCBI C++ toolkit have support for this?
libsequence provides hueristic Ka/Ks functions in C++. You could also look into in Bio++ which states that it has rate estimation routines, but I have not used it myself and can't confirm that this would be useful for you.