--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/clustalomega/clustal-omega-0.2.0/src/clustal/pair_dist.h	Tue Jun 07 17:04:25 2011 -0400
@@ -0,0 +1,42 @@
+/*********************************************************************
+ * Clustal Omega - Multiple sequence alignment
+ *
+ * Copyright (C) 2010 University College Dublin
+ *
+ * Clustal-Omega is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version.
+ *
+ * This file is part of Clustal-Omega.
+ *
+ ********************************************************************/
+
+/*
+ *  RCS $Id: pair_dist.h 193 2011-02-07 15:45:21Z andreas $
+ */
+
+
+#ifndef CLUSTALO_PAIR_DIST_H
+#define CLUSTALO_PAIR_DIST_H
+
+#define PAIRDIST_UNKNOWN 0
+/* k-tuple distances: Wilbur and Lipman (1983) */
+#define PAIRDIST_KTUPLE 1
+/* fractional identity between aligned sequences. denominator is
+ * minimum seq len (see squid:aligneval.c) */
+#define PAIRDIST_SQUIDID 2
+/* SQUIDID + Kimura correction */
+#define PAIRDIST_SQUIDID_KIMURA 3
+
+#include "seq.h"
+#include "symmatrix.h"
+
+extern int
+PairDistances(symmatrix_t **distmat, mseq_t *mseq, const int pairdist_type,
+              const int istart, const int iend,
+              const int jstart, const int jend,
+              char *fdist_in, char *fdist_out);
+
+#endif
+