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[jabaws.git] / website / archive / binaries / mac / src / clustalw / src / tree / dayhoff.h

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-/**
- * 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
-