question: 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 ; }
target:  Annotate clades of tree with posterior probability