/usr/include/clustalo/clustal/pair_dist.h is in libclustalo-dev 1.2.1-2.
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* 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 283 2013-06-10 17:42:14Z fabian $
*/
#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, bool bPercID,
const int istart, const int iend,
const int jstart, const int jend,
char *fdist_in, char *fdist_out);
#endif
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