The source posted on the Mothur page at http://www.mothur.org/wiki/Download_Clearcut
is identical to the upstream bar this one change.
I have not investigated why, but I assume it's there for a reason and
QIIME says it wants the Mothur version.
--- a/clearcut.c
+++ b/clearcut.c
@@ -1494,7 +1494,7 @@
   }
 
   NJ_output_tree2(fp, nj_args, tree, tree, dmat);
-  fprintf(fp, " ;\n");
+  fprintf(fp, ";\n");
   
   if(!nj_args->stdout_flag) {
     fclose(fp);
