public double annotate(MutableTree tree,String freqAttrName){
  annotate(tree,tree.getRoot(),freqAttrName);
  double logClade=0.0;
  for (int n=0; n < tree.getInternalNodeCount(); ++n) {
    final double f=(Double)tree.getNodeAttribute(tree.getInternalNode(n),freqAttrName);
    logClade+=Math.log(f);
  }
  return logClade;
}

public double annotate ( MutableTree tree , String freqAttrName ) { annotate ( tree , tree . getRoot ( ) , freqAttrName ) ; double logClade = 0.0 ; for ( int n = 0 ; n < tree . getInternalNodeCount ( ) ; ++ n ) { final double f = ( Double ) tree . getNodeAttribute ( tree . getInternalNode ( n ) , freqAttrName ) ; logClade += Math . log ( f ) ; } return logClade ; }
annotate clades of tree with posterior probability
