--- /dev/null
+/**
+ * Author: Mark Larkin
+ *
+ * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.
+ */
+#ifndef DAYHOFFPAMS2_H
+#define DAYHOFFPAMS2_H
+/* Mark tidy up Nov 2005 */
+/* DAYHOFF.H
+
+ Table of estimated PAMS (actual no. of substitutions per 100 residues)
+ for a range of observed amino acid distances from 75.0% (the first entry
+ in the array), in 0.1% increments, up to 93.0%.
+
+ These values are used to correct for multiple hits in protein alignments.
+ The values below are for observed distances above 74.9%. For values above
+ 93%, an arbitrary value of 1000 PAMS (1000% substitution) is used.
+
+ These values are derived from a Dayhoff model (1978) of amino acid
+ substitution and assume average amino acid composition and that amino
+ acids replace each other at the same rate as in the original Dayhoff model.
+
+ Up to 75% observed distance, use Kimura's emprical formula to derive
+ the correction. For 75% or greater, use this table. Kimura's formula
+ is accurate up to about 75% and fails completely above 85%.
+*/
+namespace clustalw
+{
+
+int dayhoff_pams[]={
+ 195, /* 75.0% observed d; 195 PAMs estimated = 195% estimated d */
+ 196, /* 75.1% observed d; 196 PAMs estimated */
+ 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, /* 250 PAMs = 80.3% observed d */
+ 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,
+ /* 92.9% observed; 945 PAMs */
+ 988 /* 93.0% observed; 988 PAMs */
+};
+}
+#endif
+