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dayhoff.h
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dayhoff.h
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/*
* dayhoff.h
*
* $Id: dayhoff.h,v 1.1 2006/08/25 03:26:44 sheneman Exp $
*
*****************************************************************************
*
* Copyright (c) 2004, Luke Sheneman
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions
* are met:
*
* + Redistributions of source code must retain the above copyright
* notice, this list of conditions and the following disclaimer.
* + Redistributions in binary form must reproduce the above copyright
* notice, this list of conditions and the following disclaimer in
* the documentation and/or other materials provided with the
* distribution.
* + The names of its contributors may not be used to endorse or promote
* products derived from this software without specific prior
* written permission.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
* POSSIBILITY OF SUCH DAMAGE.
*
*****************************************************************************
*
* AUTHOR:
*
* Luke Sheneman
* sheneman@cs.uidaho.edu
*
*/
#ifndef _INC_NJ_DAYHOFF_H_
#define _INC_NJ_DAYHOFF_H_ 1
/*
* As sequence divergence increases, we need to correct for multiple hits
* when using Kimura distance correction method for amino acid sequences.
*
* This matrix of values represents the estimated "Accepted Point Mutations"
* or PAMs for a range of amino acid sequence divergence, starting at 75%
* up through 93% (in 0.1% increments).
*
* This model is derived from Dayhoff (1978).
*
* This Dayhoff matrix and the shortcut methods for dealing with Kimura
* correction at high sequence divergence (> 75%) are derived from similar
* work in Clustal W:
*
* Thompson, J.D., Higgins, D.G., Gibson, T.J., "CLUSTAL W:
* improving the sensitivity of progressive multiple sequence
* alignment through sequence weighting, position-specific gap
* penalties and weight matrix choice.",
* Nucleic Acids Research, 22:4673-4680, 1994
*
*/
int NJ_dayhoff[]={
195, 196, 197, 198, 199, 200, 200, 201, 202, 203,
204, 205, 206, 207, 208, 209, 209, 210, 211, 212,
213, 214, 215, 216, 217, 218, 219, 220, 221, 222,
223, 224, 226, 227, 228, 229, 230, 231, 232, 233,
234, 236, 237, 238, 239, 240, 241, 243, 244, 245,
246, 248, 249, 250, 252, 253, 254, 255, 257, 258,
260, 261, 262, 264, 265, 267, 268, 270, 271, 273,
274, 276, 277, 279, 281, 282, 284, 285, 287, 289,
291, 292, 294, 296, 298, 299, 301, 303, 305, 307,
309, 311, 313, 315, 317, 319, 321, 323, 325, 328,
330, 332, 335, 337, 339, 342, 344, 347, 349, 352,
354, 357, 360, 362, 365, 368, 371, 374, 377, 380,
383, 386, 389, 393, 396, 399, 403, 407, 410, 414,
418, 422, 426, 430, 434, 438, 442, 447, 451, 456,
461, 466, 471, 476, 482, 487, 493, 498, 504, 511,
517, 524, 531, 538, 545, 553, 560, 569, 577, 586,
595, 605, 615, 626, 637, 649, 661, 675, 688, 703,
719, 736, 754, 775, 796, 819, 845, 874, 907, 945,
988
};
#endif /* _INC_NJ_DAYHOFF_H_ */