6 *****************************************************************************
8 * Copyright (c) 2004, Luke Sheneman
11 * Redistribution and use in source and binary forms, with or without
12 * modification, are permitted provided that the following conditions
15 * + Redistributions of source code must retain the above copyright
16 * notice, this list of conditions and the following disclaimer.
17 * + Redistributions in binary form must reproduce the above copyright
18 * notice, this list of conditions and the following disclaimer in
19 * the documentation and/or other materials provided with the
21 * + The names of its contributors may not be used to endorse or promote
22 * products derived from this software without specific prior
25 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
26 * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
27 * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
28 * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
29 * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
30 * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
31 * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
32 * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
33 * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
34 * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
35 * POSSIBILITY OF SUCH DAMAGE.
37 *****************************************************************************
39 * Compute a distance matrix given a set of sequences
41 *****************************************************************************
46 * sheneman@cs.uidaho.edu
52 #define _INC_DIST_H_ 1
65 * An arbitrarily large distance to represent distances
66 * which are too great to accurately correct.
68 #define NJ_BIGDIST 10.0
72 /* some function prototypes */
74 NJ_build_distance_matrix(NJ_ARGS *nj_args);
77 NJ_compute_dmat(NJ_ARGS *nj_args,
78 NJ_alignment *alignment);
82 NJ_pw_percentid(NJ_alignment *alignment,
87 NJ_pw_differences(NJ_alignment *alignment,
93 NJ_no_correction(DMAT *dmat,
94 NJ_alignment *alignment);
97 NJ_DNA_jc_correction(DMAT *dmat,
98 NJ_alignment *alignment);
101 NJ_PROTEIN_jc_correction(DMAT *dmat,
102 NJ_alignment *alignment);
105 NJ_DNA_k2p_correction(DMAT *dmat,
106 NJ_alignment *alignment);
109 NJ_PROTEIN_kimura_correction(DMAT *dmat,
110 NJ_alignment *alignment);
113 NJ_DNA_count_tt(NJ_alignment *alignment,
116 long int *transitions,
117 long int *transversions,
124 #endif /* _INC_DIST_H_ */