<BUG>for (int j = i; j < tree2.getExternalNodeCount(); j++) {</BUG><CONTEXT>index++;}}index = 0;for (int i = 0; i < tree2.getExternalNodeCount(); i++) {<extra_id_0>NodeRef nodeOne = tree2.getExternalNode(i);NodeRef nodeTwo = tree2.getExternalNode(j);NodeRef MRCA = Tree.Utils.getCommonAncestor(tree2, nodeOne, nodeTwo);</CONTEXT>
for (int j = i+1; j < tree2.getExternalNodeCount(); j++) {