A little annoyed right now with (non-) progress.
Essentially, the code downloadable from http://kimura.univ-montp2.fr/BioPP/ doesn't compile. There's a known issue with the most recent version of gcc, which is somehow a little more strict than previous versions. There are some scoping issues, which make the thing just plain not work. They know about this, but won't have the fix up until June.
It is, apparently, fixed in the "CVS" version, which I haven't gotten the chance to find yet. Pjotr set up a Git repository as I was about to start searching, and I assume that that was the same thing. However, I can't get that to compile either. It has no make file. Tried using the one from the other version, in various combinations, but couldn't get it going.
At this point I backed off, and read a bunch of material on Git. If nothing else, I feel like I understand that better.
So...current plan of attack. First, find the explicit CVS version, and make sure that that's the same as our Git version. Maybe it even has a make file in there that'll work. Second, Pjotr suggests looking at cmake, of which I hadn't heard. Looked at it briefly, and maybe it'll work better than make. The long holiday weekend is behind us, and I'll get to focus on this in the morning.