Mac binaries

[jabaws.git] / website / archive / binaries / mac / src / muscle / pam200mafft.cpp

diff --git a/website/archive/binaries/mac/src/muscle/pam200mafft.cpp b/website/archive/binaries/mac/src/muscle/pam200mafft.cpp
new file mode 100644 (file)
index 0000000..9ef24a4
--- /dev/null
+++ b/website/archive/binaries/mac/src/muscle/pam200mafft.cpp
@@ -0,0 +1,32 @@
+#include "muscle.h"\r
+\r
+// Adjusted PAM200 scoring matrix as used by default in MAFFT.\r
+//     Katoh, Misawa, Kuma and Miyata (2002), NAR 30(14), 3059-3066.\r
+\r
+static float PAM200[23][23] =\r
+       {\r
+//   A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y      B      Z      X      \r
+   408,    20,    54,    52,  -182,   179,   -68,   109,   -35,   -47,    39,   106,   206,   -14,   -12,   257,   293,   191,  -306,  -219,     0,     0,     0, // A\r
+    20,  1190,  -228,  -295,    94,     6,    63,  -131,  -184,  -176,  -112,   -29,  -122,  -195,    49,   185,    13,   -49,   199,   333,     0,     0,     0, // C\r
+    54,  -228,   645,   516,  -399,   168,    98,  -225,    75,  -341,  -235,   352,  -149,   142,   -44,    65,     7,  -147,  -418,  -128,     0,     0,     0, // D\r
+    52,  -295,   516,   630,  -460,   145,    45,  -225,   195,  -307,  -222,   186,  -121,   299,    54,   -10,   -36,  -130,  -366,  -285,     0,     0,     0, // E\r
+  -182,    94,  -399,  -460,   908,  -387,    82,   100,  -423,   340,    87,  -216,  -160,  -274,  -307,   -31,  -153,    51,    19,   604,     0,     0,     0, // F\r
+   179,     6,   168,   145,  -387,   682,   -94,  -196,   -14,  -304,  -226,    99,   -57,   -48,   117,   175,    41,   -73,   -38,  -329,     0,     0,     0, // G\r
+   -68,    63,    98,    45,    82,   -94,   786,  -185,   164,   -72,  -132,   258,    86,   388,   277,    55,   -15,  -197,  -181,   488,     0,     0,     0, // H\r
+   109,  -131,  -225,  -225,   100,  -196,  -185,   574,  -204,   308,   411,   -94,   -95,  -202,  -188,     1,   182,   489,  -254,  -133,     0,     0,     0, // I\r
+   -35,  -184,    75,   195,  -423,   -14,   164,  -204,   652,  -229,   -98,   206,   -66,   335,   486,    22,    39,  -207,  -196,  -244,     0,     0,     0, // K\r
+   -47,  -176,  -341,  -307,   340,  -304,   -72,   308,  -229,   611,   389,  -203,    73,   -66,  -150,   -49,   -21,   259,   -46,    -9,     0,     0,     0, // L\r
+    39,  -112,  -235,  -222,    87,  -226,  -132,   411,   -98,   389,   776,  -111,   -78,  -104,  -109,   -29,   149,   351,  -209,  -162,     0,     0,     0, // M\r
+   106,   -29,   352,   186,  -216,    99,   258,   -94,   206,  -203,  -111,   536,    -1,   108,    93,   260,   188,   -98,  -359,    12,     0,     0,     0, // N\r
+   206,  -122,  -149,  -121,  -160,   -57,    86,   -95,   -66,    73,   -78,    -1,   756,   142,    25,   241,   159,   -55,  -353,  -206,     0,     0,     0, // P\r
+   -14,  -195,   142,   299,  -274,   -48,   388,  -202,   335,   -66,  -104,   108,   142,   655,   321,     7,   -15,  -175,  -223,   -53,     0,     0,     0, // Q\r
+   -12,    49,   -44,    54,  -307,   117,   277,  -188,   486,  -150,  -109,    93,    25,   321,   626,    48,    16,  -181,   124,  -113,     0,     0,     0, // R\r
+   257,   185,    65,   -10,   -31,   175,    55,     1,    22,   -49,   -29,   260,   241,     7,    48,   373,   279,    28,  -193,   -35,     0,     0,     0, // S\r
+   293,    13,     7,   -36,  -153,    41,   -15,   182,    39,   -21,   149,   188,   159,   -15,    16,   279,   442,   163,  -323,  -170,     0,     0,     0, // T\r
+   191,   -49,  -147,  -130,    51,   -73,  -197,   489,  -207,   259,   351,   -98,   -55,  -175,  -181,    28,   163,   525,  -225,  -177,     0,     0,     0, // V\r
+  -306,   199,  -418,  -366,    19,   -38,  -181,  -254,  -196,   -46,  -209,  -359,  -353,  -223,   124,  -193,  -323,  -225,  1495,    83,     0,     0,     0, // W\r
+  -219,   333,  -128,  -285,   604,  -329,   488,  -133,  -244,    -9,  -162,    12,  -206,   -53,  -113,   -35,  -170,  -177,    83,   999,     0,     0,     0, // Y\r
+     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0, // B\r
+     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0, // Z\r
+     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0,     0, // X\r
+       };\r