--- /dev/null
+#include "muscle.h"\r
+\r
+#define GAPVAL 0.3\r
+#define GAPGAPVAL 5.0\r
+\r
+// Blosum62 log-average factor matrix\r
+static float Blosum62LA[20][20] =\r
+ {\r
+#define v(x) ((float) x)\r
+#define S_ROW(n, c, A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, Y) \\r
+ { v(A), v(C), v(D), v(E), v(F), v(G), v(H), v(I), v(K), v(L), v(M), v(N), v(P), v(Q), \\r
+ v(R), v(S), v(T), v(V), v(W), v(Y) },\r
+\r
+// Blosum62 log average matrix\r
+// A C D E F\r
+// G H I K L\r
+// M N P Q R\r
+// S T V W Y\r
+S_ROW( 0, 'A', 3.9029401, 0.8679881, 0.5446049, 0.7412640, 0.4648942, \r
+ 1.0568696, 0.5693654, 0.6324813, 0.7753898, 0.6019460, \r
+ 0.7231498, 0.5883077, 0.7541214, 0.7568035, 0.6126988, \r
+ 1.4721037, 0.9844022, 0.9364584, 0.4165484, 0.5426125)\r
+\r
+S_ROW( 1, 'C', 0.8679881, 19.5765802, 0.3014542, 0.2859347, 0.4389910, \r
+ 0.4203886, 0.3550472, 0.6534589, 0.3491296, 0.6422760, \r
+ 0.6113537, 0.3978026, 0.3795628, 0.3657796, 0.3089379, \r
+ 0.7384148, 0.7405530, 0.7558448, 0.4499807, 0.4342013)\r
+\r
+S_ROW( 2, 'D', 0.5446049, 0.3014542, 7.3979253, 1.6878109, 0.2989696, \r
+ 0.6343015, 0.6785593, 0.3390155, 0.7840905, 0.2866128, \r
+ 0.3464547, 1.5538520, 0.5987177, 0.8970811, 0.5732000, \r
+ 0.9135051, 0.6947898, 0.3365004, 0.2321050, 0.3456829)\r
+\r
+S_ROW( 3, 'E', 0.7412640, 0.2859347, 1.6878109, 5.4695276, 0.3307441, \r
+ 0.4812675, 0.9600400, 0.3305223, 1.3082782, 0.3728734, \r
+ 0.5003421, 0.9112983, 0.6792027, 1.9017376, 0.9607983, \r
+ 0.9503570, 0.7414260, 0.4289431, 0.3743021, 0.4964664)\r
+\r
+S_ROW( 4, 'F', 0.4648942, 0.4389910, 0.2989696, 0.3307441, 8.1287983, \r
+ 0.3406407, 0.6519893, 0.9457698, 0.3440433, 1.1545978, \r
+ 1.0043715, 0.3542882, 0.2874440, 0.3339729, 0.3807263, \r
+ 0.4399736, 0.4816930, 0.7450894, 1.3743775, 2.7693817)\r
+\r
+S_ROW( 5, 'G', 1.0568696, 0.4203886, 0.6343015, 0.4812675, 0.3406407, \r
+ 6.8763075, 0.4929663, 0.2750096, 0.5888716, 0.2845039, \r
+ 0.3954865, 0.8637114, 0.4773858, 0.5386498, 0.4499840, \r
+ 0.9035965, 0.5792712, 0.3369551, 0.4216898, 0.3487141)\r
+\r
+S_ROW( 6, 'H', 0.5693654, 0.3550472, 0.6785593, 0.9600400, 0.6519893, \r
+ 0.4929663, 13.5060070, 0.3262878, 0.7788884, 0.3806759, \r
+ 0.5841316, 1.2220028, 0.4728797, 1.1679835, 0.9170473, \r
+ 0.7367319, 0.5575021, 0.3394474, 0.4440859, 1.7979036)\r
+\r
+S_ROW( 7, 'I', 0.6324813, 0.6534589, 0.3390155, 0.3305223, 0.9457698, \r
+ 0.2750096, 0.3262878, 3.9979299, 0.3963730, 1.6944349, \r
+ 1.4777449, 0.3279345, 0.3846629, 0.3829375, 0.3547509, \r
+ 0.4431634, 0.7798163, 2.4175121, 0.4088732, 0.6303898)\r
+\r
+S_ROW( 8, 'K', 0.7753898, 0.3491296, 0.7840905, 1.3082782, 0.3440433, \r
+ 0.5888716, 0.7788884, 0.3963730, 4.7643359, 0.4282702, \r
+ 0.6253033, 0.9398419, 0.7037741, 1.5543233, 2.0768092, \r
+ 0.9319192, 0.7929060, 0.4565429, 0.3589319, 0.5321784)\r
+\r
+S_ROW( 9, 'L', 0.6019460, 0.6422760, 0.2866128, 0.3728734, 1.1545978, \r
+ 0.2845039, 0.3806759, 1.6944349, 0.4282702, 3.7966214, \r
+ 1.9942957, 0.3100430, 0.3711219, 0.4773261, 0.4739194, \r
+ 0.4288939, 0.6603292, 1.3142355, 0.5680359, 0.6920589)\r
+\r
+S_ROW(10, 'M', 0.7231498, 0.6113537, 0.3464547, 0.5003421, 1.0043715, \r
+ 0.3954865, 0.5841316, 1.4777449, 0.6253033, 1.9942957, \r
+ 6.4814549, 0.4745299, 0.4238960, 0.8642486, 0.6226249, \r
+ 0.5985578, 0.7938018, 1.2689365, 0.6103022, 0.7083636)\r
+\r
+S_ROW(11, 'N', 0.5883077, 0.3978026, 1.5538520, 0.9112983, 0.3542882, \r
+ 0.8637114, 1.2220028, 0.3279345, 0.9398419, 0.3100430, \r
+ 0.4745299, 7.0940964, 0.4999337, 1.0005835, 0.8586298, \r
+ 1.2315289, 0.9841525, 0.3690340, 0.2777841, 0.4860309)\r
+\r
+S_ROW(12, 'P', 0.7541214, 0.3795628, 0.5987177, 0.6792027, 0.2874440, \r
+ 0.4773858, 0.4728797, 0.3846629, 0.7037741, 0.3711219, \r
+ 0.4238960, 0.4999337, 12.8375452, 0.6412803, 0.4815348, \r
+ 0.7555033, 0.6888962, 0.4430825, 0.2818321, 0.3635216)\r
+\r
+S_ROW(13, 'Q', 0.7568035, 0.3657796, 0.8970811, 1.9017376, 0.3339729, \r
+ 0.5386498, 1.1679835, 0.3829375, 1.5543233, 0.4773261, \r
+ 0.8642486, 1.0005835, 0.6412803, 6.2444210, 1.4057958, \r
+ 0.9655559, 0.7913219, 0.4667781, 0.5093584, 0.6110951)\r
+\r
+S_ROW(14, 'R', 0.6126988, 0.3089379, 0.5732000, 0.9607983, 0.3807263, \r
+ 0.4499840, 0.9170473, 0.3547509, 2.0768092, 0.4739194, \r
+ 0.6226249, 0.8586298, 0.4815348, 1.4057958, 6.6655769, \r
+ 0.7671661, 0.6777544, 0.4200721, 0.3951049, 0.5559652)\r
+\r
+S_ROW(15, 'S', 1.4721037, 0.7384148, 0.9135051, 0.9503570, 0.4399736, \r
+ 0.9035965, 0.7367319, 0.4431634, 0.9319192, 0.4288939, \r
+ 0.5985578, 1.2315289, 0.7555033, 0.9655559, 0.7671661, \r
+ 3.8428476, 1.6139205, 0.5652240, 0.3853031, 0.5575206)\r
+\r
+S_ROW(16, 'T', 0.9844022, 0.7405530, 0.6947898, 0.7414260, 0.4816930, \r
+ 0.5792712, 0.5575021, 0.7798163, 0.7929060, 0.6603292, \r
+ 0.7938018, 0.9841525, 0.6888962, 0.7913219, 0.6777544, \r
+ 1.6139205, 4.8321048, 0.9809432, 0.4309317, 0.5731577)\r
+\r
+S_ROW(17, 'V', 0.9364584, 0.7558448, 0.3365004, 0.4289431, 0.7450894, \r
+ 0.3369551, 0.3394474, 2.4175121, 0.4565429, 1.3142355, \r
+ 1.2689365, 0.3690340, 0.4430825, 0.4667781, 0.4200721, \r
+ 0.5652240, 0.9809432, 3.6921553, 0.3744576, 0.6580390)\r
+\r
+S_ROW(18, 'W', 0.4165484, 0.4499807, 0.2321050, 0.3743021, 1.3743775, \r
+ 0.4216898, 0.4440859, 0.4088732, 0.3589319, 0.5680359, \r
+ 0.6103022, 0.2777841, 0.2818321, 0.5093584, 0.3951049, \r
+ 0.3853031, 0.4309317, 0.3744576, 38.1077830, 2.1098056)\r
+\r
+S_ROW(19, 'Y', 0.5426125, 0.4342013, 0.3456829, 0.4964664, 2.7693817, \r
+ 0.3487141, 1.7979036, 0.6303898, 0.5321784, 0.6920589, \r
+ 0.7083636, 0.4860309, 0.3635216, 0.6110951, 0.5559652, \r
+ 0.5575206, 0.5731577, 0.6580390, 2.1098056, 9.8322054)\r
+ };\r
git://source.jalview.org / jabaws.git / blobdiff