I don't know for sure if it's the best diff algorithms but you might want to check out those links that talks about SOCT4 and SOCT6
http://dev.libresource.org/home/doc/so6-user-manual/concepts
and also:
http://www.loria.fr/~molli/pmwiki/uploads/Main/so6group03.pdf
http://www.loria.fr/~molli/pmwiki/uploads/Main/diffalgo.pdf