--- /dev/null
+#ifndef GOTOHOVERLAP_H
+#define GOTOHOVERLAP_H
+
+/*
+ * gotohoverlap.h
+ *
+ *
+ * Created by Pat Schloss on 12/15/08.
+ * Copyright 2008 Patrick D. Schloss. All rights reserved.
+ *
+ * This class is an Alignment child class that implements the Gotoh pairwise alignment algorithm as described in:
+ *
+ * Gotoh O. 1982. An improved algorithm for matching biological sequences. J. Mol. Biol. 162:705-8.
+ * Myers, EW & Miller, W. 1988. Optimal alignments in linear space. Comput Appl Biosci. 4:11-7.
+ *
+ * This method is nice because it allows for an affine gap penalty to be assessed, which is analogous to what is used
+ * in blast and is an alternative to Needleman-Wunsch, which only charges the same penalty for each gap position.
+ * Because this method typically has problems at the ends when two sequences do not full overlap, we employ a separate
+ * method to fix the ends (see Overlap class documentation)
+ *
+ */
+
+#include "mothur.h"
+#include "alignment.hpp"
+
+/**************************************************************************************************/
+
+class GotohOverlap : public Alignment {
+
+public:
+ GotohOverlap(float, float, float, float, int);
+ void align(string, string);
+
+private:
+ float gapOpen;
+ float gapExtend;
+ float match;
+ float mismatch;
+};
+
+/**************************************************************************************************/
+
+#endif