--- /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