+ * Gets the mapping for sequences with their associated tree nodes
+ *
+ * @return
+ */
+ public Map<SequenceI, TreeNodeI> getAlignmentWithNodes();
+
+ /**
+ * Gets the mapping for tree nodes with their associated sequences
+ *
+ * @return
+ */
+ public Map<TreeNodeI, SequenceI> getNodesWithAlignment();
+
+ /**
+ *
+ * @param x
+ * coordinate that functions as the clustering threshold
+ */
+ public void partitionTree(final int x);
+
+ public void showMatchingChildSequences(TreeNodeI parentNode);
+
+ public void showMatchingSequence(TreeNodeI nodeToMatch);
+
+ /**