+++ /dev/null
-/*
- * dayhoff.h
- *
- * $Id$
- *
- *****************************************************************************
- *
- * 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_ */
-
-
-
projects / mothur.git / blobdiff