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 *****************************************************************************
42 * sheneman@cs.uidaho.edu
47 #ifndef _INC_NJ_DAYHOFF_H_
48 #define _INC_NJ_DAYHOFF_H_ 1
51 * As sequence divergence increases, we need to correct for multiple hits
52 * when using Kimura distance correction method for amino acid sequences.
54 * This matrix of values represents the estimated "Accepted Point Mutations"
55 * or PAMs for a range of amino acid sequence divergence, starting at 75%
56 * up through 93% (in 0.1% increments).
58 * This model is derived from Dayhoff (1978).
60 * This Dayhoff matrix and the shortcut methods for dealing with Kimura
61 * correction at high sequence divergence (> 75%) are derived from similar
64 * Thompson, J.D., Higgins, D.G., Gibson, T.J., "CLUSTAL W:
65 * improving the sensitivity of progressive multiple sequence
66 * alignment through sequence weighting, position-specific gap
67 * penalties and weight matrix choice.",
68 * Nucleic Acids Research, 22:4673-4680, 1994
74 195, 196, 197, 198, 199, 200, 200, 201, 202, 203,
75 204, 205, 206, 207, 208, 209, 209, 210, 211, 212,
76 213, 214, 215, 216, 217, 218, 219, 220, 221, 222,
77 223, 224, 226, 227, 228, 229, 230, 231, 232, 233,
78 234, 236, 237, 238, 239, 240, 241, 243, 244, 245,
79 246, 248, 249, 250, 252, 253, 254, 255, 257, 258,
80 260, 261, 262, 264, 265, 267, 268, 270, 271, 273,
81 274, 276, 277, 279, 281, 282, 284, 285, 287, 289,
82 291, 292, 294, 296, 298, 299, 301, 303, 305, 307,
83 309, 311, 313, 315, 317, 319, 321, 323, 325, 328,
84 330, 332, 335, 337, 339, 342, 344, 347, 349, 352,
85 354, 357, 360, 362, 365, 368, 371, 374, 377, 380,
86 383, 386, 389, 393, 396, 399, 403, 407, 410, 414,
87 418, 422, 426, 430, 434, 438, 442, 447, 451, 456,
88 461, 466, 471, 476, 482, 487, 493, 498, 504, 511,
89 517, 524, 531, 538, 545, 553, 560, 569, 577, 586,
90 595, 605, 615, 626, 637, 649, 661, 675, 688, 703,
91 719, 736, 754, 775, 796, 819, 845, 874, 907, 945,
97 #endif /* _INC_NJ_DAYHOFF_H_ */