TreeAnnotator allows specification of burnin as number of states or number of trees (UI has radio button). The command line option -burnin now uses number of states (as the help has always suggested) but this is complemented by a -burninTrees option.

git-svn-id: http://beast-mcmc.googlecode.com/svn@6528 ca793f91-a31e-0410-b540-2769d408b6a1