biotite 1.5.0__cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl

biotite/sequence/align/matrix_data/PAM50.mat

@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 50 substitution matrix, scale = ln(2)/2 = 0.346574
+#
+# Expected score = -3.70, Entropy = 2.00 bits
+#
+# Lowest score = -13, Highest score = 13
+#
+    A   R   N   D   C   Q   E   G   H   I   L   K   M   F   P   S   T   W   Y   V   B   Z   X   *
+A   5  -5  -2  -2  -5  -3  -1  -1  -5  -3  -5  -5  -4  -7   0   0   0 -11  -6  -1  -2  -2  -2 -13
+R  -5   8  -4  -7  -6   0  -7  -7   0  -4  -7   1  -3  -8  -3  -2  -5  -1  -8  -6  -5  -2  -4 -13
+N  -2  -4   7   2  -8  -2  -1  -2   1  -4  -6   0  -6  -7  -4   1  -1  -7  -3  -6   5  -1  -2 -13
+D  -2  -7   2   7 -11  -1   3  -2  -2  -6 -10  -3  -8 -12  -6  -2  -3 -12  -9  -6   6   2  -4 -13
+C  -5  -6  -8 -11   9 -11 -11  -7  -6  -5 -12 -11 -11 -10  -6  -2  -6 -13  -3  -5  -9 -11  -7 -13
+Q  -3   0  -2  -1 -11   8   2  -5   2  -6  -4  -2  -3 -10  -2  -4  -4 -10  -9  -5  -2   6  -3 -13
+E  -1  -7  -1   3 -11   2   7  -3  -3  -4  -7  -3  -5 -11  -4  -3  -4 -13  -7  -5   2   6  -3 -13
+G  -1  -7  -2  -2  -7  -5  -3   6  -7  -8  -9  -6  -7  -8  -4  -1  -4 -12 -11  -4  -2  -4  -4 -13
+H  -5   0   1  -2  -6   2  -3  -7   9  -7  -5  -4  -8  -5  -3  -4  -5  -6  -2  -5   0   0  -4 -13
+I  -3  -4  -4  -6  -5  -6  -4  -8  -7   8   0  -5   0  -1  -7  -5  -1 -11  -5   3  -5  -5  -3 -13
+L  -5  -7  -6 -10 -12  -4  -7  -9  -5   0   6  -6   2  -1  -6  -7  -5  -5  -5  -1  -7  -5  -5 -13
+K  -5   1   0  -3 -11  -2  -3  -6  -4  -5  -6   6  -1 -11  -5  -3  -2  -9  -8  -7  -1  -2  -4 -13
+M  -4  -3  -6  -8 -11  -3  -5  -7  -8   0   2  -1  10  -3  -6  -4  -3 -10  -8   0  -7  -4  -4 -13
+F  -7  -8  -7 -12 -10 -10 -11  -8  -5  -1  -1 -11  -3   9  -8  -5  -7  -3   3  -6  -9 -11  -6 -13
+P   0  -3  -4  -6  -6  -2  -4  -4  -3  -7  -6  -5  -6  -8   8  -1  -3 -11 -11  -4  -5  -3  -4 -13
+S   0  -2   1  -2  -2  -4  -3  -1  -4  -5  -7  -3  -4  -5  -1   6   1  -4  -5  -4  -1  -3  -2 -13
+T   0  -5  -1  -3  -6  -4  -4  -4  -5  -1  -5  -2  -3  -7  -3   1   6 -10  -5  -2  -2  -4  -2 -13
+W -11  -1  -7 -12 -13 -10 -13 -12  -6 -11  -5  -9 -10  -3 -11  -4 -10  13  -4 -12  -8 -11  -9 -13
+Y  -6  -8  -3  -9  -3  -9  -7 -11  -2  -5  -5  -8  -8   3 -11  -5  -5  -4   9  -6  -5  -8  -6 -13
+V  -1  -6  -6  -6  -5  -5  -5  -4  -5   3  -1  -7   0  -6  -4  -4  -2 -12  -6   7  -6  -5  -3 -13
+B  -2  -5   5   6  -9  -2   2  -2   0  -5  -7  -1  -7  -9  -5  -1  -2  -8  -5  -6   5   1  -3 -13
+Z  -2  -2  -1   2 -11   6   6  -4   0  -5  -5  -2  -4 -11  -3  -3  -4 -11  -8  -5   1   6  -3 -13
+X  -2  -4  -2  -4  -7  -3  -3  -4  -4  -3  -5  -4  -4  -6  -4  -2  -2  -9  -6  -3  -3  -3  -4 -13
+* -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13   1

biotite/sequence/align/matrix_data/PAM500.mat

@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 500 substitution matrix, scale = ln(2)/7 = 0.0990210
+#
+# Expected score = -0.401, Entropy = 0.0803 bits
+#
+# Lowest score = -9, Highest score = 34
+#
+   A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V  B  Z  X  *
+A  1 -1  0  1 -2  0  1  1  0  0 -1  0 -1 -3  1  1  1 -6 -3  0  1  0  0 -9
+R -1  5  1  0 -4  2  0 -1  2 -2 -2  4  0 -4  0  0  0  4 -4 -2  0  1  0 -9
+N  0  1  1  2 -3  1  1  1  1 -1 -2  1 -1 -4  0  1  0 -5 -3 -1  1  1  0 -9
+D  1  0  2  3 -5  2  3  1  1 -2 -3  1 -2 -5  0  1  0 -7 -5 -1  2  2  0 -9
+C -2 -4 -3 -5 22 -5 -5 -3 -4 -2 -6 -5 -5 -3 -2  0 -2 -9  2 -2 -4 -5 -2 -9
+Q  0  2  1  2 -5  2  2  0  2 -1 -2  1 -1 -4  1  0  0 -5 -4 -1  2  2  0 -9
+E  1  0  1  3 -5  2  3  1  1 -2 -3  1 -1 -5  0  1  0 -7 -5 -1  2  2  0 -9
+G  1 -1  1  1 -3  0  1  4 -1 -2 -3  0 -2 -5  1  1  1 -8 -5 -1  1  1  0 -9
+H  0  2  1  1 -4  2  1 -1  4 -2 -2  1 -1 -2  0  0  0 -2  0 -2  1  2  0 -9
+I  0 -2 -1 -2 -2 -1 -2 -2 -2  3  4 -2  3  2 -1 -1  0 -5  0  3 -2 -2  0 -9
+L -1 -2 -2 -3 -6 -2 -3 -3 -2  4  7 -2  4  4 -2 -2 -1 -1  1  3 -3 -2 -1 -9
+K  0  4  1  1 -5  1  1  0  1 -2 -2  4  0 -5  0  0  0 -3 -5 -2  1  1  0 -9
+M -1  0 -1 -2 -5 -1 -1 -2 -1  3  4  0  4  1 -1 -1  0 -4 -1  2 -1 -1  0 -9
+F -3 -4 -4 -5 -3 -4 -5 -5 -2  2  4 -5  1 13 -4 -3 -3  3 13  0 -4 -5 -2 -9
+P  1  0  0  0 -2  1  0  1  0 -1 -2  0 -1 -4  4  1  1 -6 -5 -1  0  1  0 -9
+S  1  0  1  1  0  0  1  1  0 -1 -2  0 -1 -3  1  1  1 -3 -3 -1  1  0  0 -9
+T  1  0  0  0 -2  0  0  1  0  0 -1  0  0 -3  1  1  1 -6 -3  0  0  0  0 -9
+W -6  4 -5 -7 -9 -5 -7 -8 -2 -5 -1 -3 -4  3 -6 -3 -6 34  2 -6 -6 -6 -4 -9
+Y -3 -4 -3 -5  2 -4 -5 -5  0  0  1 -5 -1 13 -5 -3 -3  2 15 -1 -4 -4 -2 -9
+V  0 -2 -1 -1 -2 -1 -1 -1 -2  3  3 -2  2  0 -1 -1  0 -6 -1  3 -1 -1  0 -9
+B  1  0  1  2 -4  2  2  1  1 -2 -3  1 -1 -4  0  1  0 -6 -4 -1  2  2  0 -9
+Z  0  1  1  2 -5  2  2  1  2 -2 -2  1 -1 -5  1  0  0 -6 -4 -1  2  2  0 -9
+X  0  0  0  0 -2  0  0  0  0  0 -1  0  0 -2  0  0  0 -4 -2  0  0  0  0 -9
+* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9  1

biotite/sequence/align/matrix_data/PAM60.mat

@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 60 substitution matrix, scale = ln(2)/2 = 0.346574
+#
+# Expected score = -3.21, Entropy = 1.79 bits
+#
+# Lowest score = -12, Highest score = 13
+#
+    A   R   N   D   C   Q   E   G   H   I   L   K   M   F   P   S   T   W   Y   V   B   Z   X   *
+A   5  -5  -2  -2  -5  -3  -1   0  -5  -3  -4  -5  -3  -6   0   1   1 -10  -6  -1  -2  -2  -2 -12
+R  -5   8  -3  -6  -6   0  -6  -7   0  -4  -6   2  -2  -7  -2  -2  -4   0  -8  -5  -5  -2  -4 -12
+N  -2  -3   6   2  -7  -2   0  -1   1  -4  -5   0  -6  -6  -4   1  -1  -6  -3  -5   5  -1  -2 -12
+D  -2  -6   2   7 -10  -1   3  -2  -2  -5  -9  -2  -7 -11  -5  -2  -3 -11  -8  -6   5   2  -3 -12
+C  -5  -6  -7 -10   9 -10 -10  -7  -6  -4 -11 -10 -10  -9  -6  -1  -5 -12  -2  -4  -9 -10  -6 -12
+Q  -3   0  -2  -1 -10   7   2  -5   2  -5  -3  -1  -2  -9  -1  -3  -4  -9  -8  -5  -1   6  -3 -12
+E  -1  -6   0   3 -10   2   7  -2  -3  -4  -7  -3  -5 -10  -3  -2  -4 -12  -7  -4   2   5  -3 -12
+G   0  -7  -1  -2  -7  -5  -2   6  -6  -7  -8  -5  -6  -7  -4   0  -3 -11 -10  -4  -2  -3  -3 -12
+H  -5   0   1  -2  -6   2  -3  -6   8  -6  -4  -4  -7  -4  -2  -4  -5  -5  -2  -5   0   0  -3 -12
+I  -3  -4  -4  -5  -4  -5  -4  -7  -6   7   0  -4   1  -1  -6  -4  -1 -10  -4   3  -4  -4  -3 -12
+L  -4  -6  -5  -9 -11  -3  -7  -8  -4   0   6  -6   2  -1  -5  -6  -5  -4  -5  -1  -7  -5  -4 -12
+K  -5   2   0  -2 -10  -1  -3  -5  -4  -4  -6   6   0 -10  -4  -2  -2  -8  -7  -6  -1  -2  -3 -12
+M  -3  -2  -6  -7 -10  -2  -5  -6  -7   1   2   0  10  -2  -6  -4  -2  -9  -7   0  -6  -4  -3 -12
+F  -6  -7  -6 -11  -9  -9 -10  -7  -4  -1  -1 -10  -2   8  -7  -5  -6  -3   3  -5  -8 -10  -5 -12
+P   0  -2  -4  -5  -6  -1  -3  -4  -2  -6  -5  -4  -6  -7   7   0  -2 -10 -10  -4  -4  -2  -3 -12
+S   1  -2   1  -2  -1  -3  -2   0  -4  -4  -6  -2  -4  -5   0   5   1  -4  -5  -4   0  -3  -2 -12
+T   1  -4  -1  -3  -5  -4  -4  -3  -5  -1  -5  -2  -2  -6  -2   1   6  -9  -5  -1  -2  -4  -2 -12
+W -10   0  -6 -11 -12  -9 -12 -11  -5 -10  -4  -8  -9  -3 -10  -4  -9  13  -3 -11  -8 -11  -8 -12
+Y  -6  -8  -3  -8  -2  -8  -7 -10  -2  -4  -5  -7  -7   3 -10  -5  -5  -3   9  -5  -5  -7  -5 -12
+V  -1  -5  -5  -6  -4  -5  -4  -4  -5   3  -1  -6   0  -5  -4  -4  -1 -11  -5   6  -5  -5  -3 -12
+B  -2  -5   5   5  -9  -1   2  -2   0  -4  -7  -1  -6  -8  -4   0  -2  -8  -5  -5   5   1  -3 -12
+Z  -2  -2  -1   2 -10   6   5  -3   0  -4  -5  -2  -4 -10  -2  -3  -4 -11  -7  -5   1   5  -3 -12
+X  -2  -4  -2  -3  -6  -3  -3  -3  -3  -3  -4  -3  -3  -5  -3  -2  -2  -8  -5  -3  -3  -3  -3 -12
+* -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12   1

biotite/sequence/align/matrix_data/PAM70.mat

@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 70 substitution matrix, scale = ln(2)/2 = 0.346574
+#
+# Expected score = -2.77, Entropy = 1.60 bits
+#
+# Lowest score = -11, Highest score = 13
+#
+    A   R   N   D   C   Q   E   G   H   I   L   K   M   F   P   S   T   W   Y   V   B   Z   X   *
+A   5  -4  -2  -1  -4  -2  -1   0  -4  -2  -4  -4  -3  -6   0   1   1  -9  -5  -1  -1  -1  -2 -11
+R  -4   8  -3  -6  -5   0  -5  -6   0  -3  -6   2  -2  -7  -2  -1  -4   0  -7  -5  -4  -2  -3 -11
+N  -2  -3   6   3  -7  -1   0  -1   1  -3  -5   0  -5  -6  -3   1   0  -6  -3  -5   5  -1  -2 -11
+D  -1  -6   3   6  -9   0   3  -1  -1  -5  -8  -2  -7 -10  -4  -1  -2 -10  -7  -5   5   2  -3 -11
+C  -4  -5  -7  -9   9  -9  -9  -6  -5  -4 -10  -9  -9  -8  -5  -1  -5 -11  -2  -4  -8  -9  -6 -11
+Q  -2   0  -1   0  -9   7   2  -4   2  -5  -3  -1  -2  -9  -1  -3  -3  -8  -8  -4  -1   5  -2 -11
+E  -1  -5   0   3  -9   2   6  -2  -2  -4  -6  -2  -4  -9  -3  -2  -3 -11  -6  -4   2   5  -3 -11
+G   0  -6  -1  -1  -6  -4  -2   6  -6  -6  -7  -5  -6  -7  -3   0  -3 -10  -9  -3  -1  -3  -3 -11
+H  -4   0   1  -1  -5   2  -2  -6   8  -6  -4  -3  -6  -4  -2  -3  -4  -5  -1  -4   0   1  -3 -11
+I  -2  -3  -3  -5  -4  -5  -4  -6  -6   7   1  -4   1   0  -5  -4  -1  -9  -4   3  -4  -4  -3 -11
+L  -4  -6  -5  -8 -10  -3  -6  -7  -4   1   6  -5   2  -1  -5  -6  -4  -4  -4   0  -6  -4  -4 -11
+K  -4   2   0  -2  -9  -1  -2  -5  -3  -4  -5   6   0  -9  -4  -2  -1  -7  -7  -6  -1  -2  -3 -11
+M  -3  -2  -5  -7  -9  -2  -4  -6  -6   1   2   0  10  -2  -5  -3  -2  -8  -7   0  -6  -3  -3 -11
+F  -6  -7  -6 -10  -8  -9  -9  -7  -4   0  -1  -9  -2   8  -7  -4  -6  -2   4  -5  -7  -9  -5 -11
+P   0  -2  -3  -4  -5  -1  -3  -3  -2  -5  -5  -4  -5  -7   7   0  -2  -9  -9  -3  -4  -2  -3 -11
+S   1  -1   1  -1  -1  -3  -2   0  -3  -4  -6  -2  -3  -4   0   5   2  -3  -5  -3   0  -2  -1 -11
+T   1  -4   0  -2  -5  -3  -3  -3  -4  -1  -4  -1  -2  -6  -2   2   6  -8  -4  -1  -1  -3  -2 -11
+W  -9   0  -6 -10 -11  -8 -11 -10  -5  -9  -4  -7  -8  -2  -9  -3  -8  13  -3 -10  -7 -10  -7 -11
+Y  -5  -7  -3  -7  -2  -8  -6  -9  -1  -4  -4  -7  -7   4  -9  -5  -4  -3   9  -5  -4  -7  -5 -11
+V  -1  -5  -5  -5  -4  -4  -4  -3  -4   3   0  -6   0  -5  -3  -3  -1 -10  -5   6  -5  -4  -2 -11
+B  -1  -4   5   5  -8  -1   2  -1   0  -4  -6  -1  -6  -7  -4   0  -1  -7  -4  -5   5   1  -2 -11
+Z  -1  -2  -1   2  -9   5   5  -3   1  -4  -4  -2  -3  -9  -2  -2  -3 -10  -7  -4   1   5  -3 -11
+X  -2  -3  -2  -3  -6  -2  -3  -3  -3  -3  -4  -3  -3  -5  -3  -1  -2  -7  -5  -2  -2  -3  -3 -11
+* -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11   1

biotite/sequence/align/matrix_data/PAM80.mat

@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 80 substitution matrix, scale = ln(2)/2 = 0.346574
+#
+# Expected score = -2.55, Entropy = 1.44 bits
+#
+# Lowest score = -11, Highest score = 13
+#
+    A   R   N   D   C   Q   E   G   H   I   L   K   M   F   P   S   T   W   Y   V   B   Z   X   *
+A   4  -4  -1  -1  -4  -2  -1   0  -4  -2  -4  -4  -3  -5   0   1   1  -8  -5   0  -1  -1  -1 -11
+R  -4   7  -2  -5  -5   0  -4  -6   0  -3  -5   2  -2  -6  -2  -1  -3   0  -7  -5  -3  -1  -3 -11
+N  -1  -2   5   3  -6  -1   0  -1   2  -3  -5   0  -4  -5  -3   1   0  -5  -3  -4   4   0  -1 -11
+D  -1  -5   3   6  -9   0   4  -1  -1  -4  -7  -2  -6  -9  -4  -1  -2 -10  -7  -5   5   2  -3 -11
+C  -4  -5  -6  -9   9  -9  -9  -6  -5  -4  -9  -9  -8  -8  -5  -1  -4 -10  -2  -3  -7  -9  -5 -11
+Q  -2   0  -1   0  -9   7   2  -4   2  -4  -3  -1  -2  -8  -1  -3  -3  -8  -7  -4   0   5  -2 -11
+E  -1  -4   0   4  -9   2   6  -2  -2  -3  -6  -2  -4  -9  -3  -2  -3 -11  -6  -4   2   5  -2 -11
+G   0  -6  -1  -1  -6  -4  -2   6  -5  -6  -7  -4  -5  -6  -3   0  -2 -10  -8  -3  -1  -2  -3 -11
+H  -4   0   2  -1  -5   2  -2  -5   8  -5  -4  -3  -5  -3  -2  -3  -4  -4  -1  -4   0   1  -2 -11
+I  -2  -3  -3  -4  -4  -4  -3  -6  -5   7   1  -4   1   0  -5  -4  -1  -8  -3   3  -4  -4  -2 -11
+L  -4  -5  -5  -7  -9  -3  -6  -7  -4   1   6  -5   2   0  -4  -5  -4  -3  -4   0  -6  -4  -3 -11
+K  -4   2   0  -2  -9  -1  -2  -4  -3  -4  -5   6   0  -9  -4  -2  -1  -7  -6  -5  -1  -1  -3 -11
+M  -3  -2  -4  -6  -8  -2  -4  -5  -5   1   2   0   9  -2  -5  -3  -2  -7  -6   1  -5  -3  -2 -11
+F  -5  -6  -5  -9  -8  -8  -9  -6  -3   0   0  -9  -2   8  -7  -4  -5  -2   4  -4  -7  -8  -5 -11
+P   0  -2  -3  -4  -5  -1  -3  -3  -2  -5  -4  -4  -5  -7   7   0  -2  -9  -8  -3  -3  -2  -2 -11
+S   1  -1   1  -1  -1  -3  -2   0  -3  -4  -5  -2  -3  -4   0   4   2  -3  -4  -3   0  -2  -1 -11
+T   1  -3   0  -2  -4  -3  -3  -2  -4  -1  -4  -1  -2  -5  -2   2   5  -8  -4  -1  -1  -3  -1 -11
+W  -8   0  -5 -10 -10  -8 -11 -10  -4  -8  -3  -7  -7  -2  -9  -3  -8  13  -2 -10  -7  -9  -7 -11
+Y  -5  -7  -3  -7  -2  -7  -6  -8  -1  -3  -4  -6  -6   4  -8  -4  -4  -2   9  -5  -4  -6  -4 -11
+V   0  -5  -4  -5  -3  -4  -4  -3  -4   3   0  -5   1  -4  -3  -3  -1 -10  -5   6  -4  -4  -2 -11
+B  -1  -3   4   5  -7   0   2  -1   0  -4  -6  -1  -5  -7  -3   0  -1  -7  -4  -4   5   2  -2 -11
+Z  -1  -1   0   2  -9   5   5  -2   1  -4  -4  -1  -3  -8  -2  -2  -3  -9  -6  -4   2   5  -2 -11
+X  -1  -3  -1  -3  -5  -2  -2  -3  -2  -2  -3  -3  -2  -5  -2  -1  -1  -7  -4  -2  -2  -2  -3 -11
+* -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11   1

biotite/sequence/align/matrix_data/PAM90.mat

@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 90 substitution matrix, scale = ln(2)/2 = 0.346574
+#
+# Expected score = -2.26, Entropy = 1.30 bits
+#
+# Lowest score = -10, Highest score = 13
+#
+    A   R   N   D   C   Q   E   G   H   I   L   K   M   F   P   S   T   W   Y   V   B   Z   X   *
+A   4  -4  -1  -1  -3  -2   0   0  -4  -2  -3  -3  -2  -5   0   1   1  -8  -5   0  -1  -1  -1 -10
+R  -4   7  -2  -5  -5   0  -4  -5   1  -3  -5   2  -2  -6  -1  -1  -3   0  -6  -4  -3  -1  -2 -10
+N  -1  -2   5   3  -6  -1   0  -1   2  -3  -4   1  -4  -5  -2   1   0  -5  -2  -4   4   0  -1 -10
+D  -1  -5   3   6  -8   0   4  -1  -1  -4  -7  -2  -5  -8  -4  -1  -2  -9  -6  -4   5   3  -2 -10
+C  -3  -5  -6  -8   9  -8  -8  -5  -5  -3  -9  -8  -8  -7  -5  -1  -4 -10  -1  -3  -7  -8  -5 -10
+Q  -2   0  -1   0  -8   6   2  -3   2  -4  -3  -1  -2  -7  -1  -2  -3  -7  -6  -4   0   5  -2 -10
+E   0  -4   0   4  -8   2   6  -1  -1  -3  -5  -2  -4  -8  -2  -2  -2 -10  -6  -3   2   5  -2 -10
+G   0  -5  -1  -1  -5  -3  -1   5  -5  -5  -6  -4  -5  -6  -3   0  -2  -9  -8  -3  -1  -2  -2 -10
+H  -4   1   2  -1  -5   2  -1  -5   8  -5  -3  -2  -5  -3  -2  -3  -3  -4  -1  -4   1   1  -2 -10
+I  -2  -3  -3  -4  -3  -4  -3  -5  -5   6   1  -3   1   0  -4  -3   0  -8  -3   3  -3  -3  -2 -10
+L  -3  -5  -4  -7  -9  -3  -5  -6  -3   1   6  -5   2   0  -4  -5  -3  -3  -3   0  -5  -4  -3 -10
+K  -3   2   1  -2  -8  -1  -2  -4  -2  -3  -5   5   0  -8  -3  -1  -1  -6  -6  -5   0  -1  -2 -10
+M  -2  -2  -4  -5  -8  -2  -4  -5  -5   1   2   0   9  -1  -4  -3  -2  -7  -6   1  -5  -3  -2 -10
+F  -5  -6  -5  -8  -7  -7  -8  -6  -3   0   0  -8  -1   8  -6  -4  -5  -2   4  -4  -6  -8  -4 -10
+P   0  -1  -2  -4  -5  -1  -2  -3  -2  -4  -4  -3  -4  -6   7   0  -1  -8  -8  -3  -3  -2  -2 -10
+S   1  -1   1  -1  -1  -2  -2   0  -3  -3  -5  -1  -3  -4   0   4   2  -3  -4  -3   0  -2  -1 -10
+T   1  -3   0  -2  -4  -3  -2  -2  -3   0  -3  -1  -2  -5  -1   2   5  -7  -4  -1  -1  -2  -1 -10
+W  -8   0  -5  -9 -10  -7 -10  -9  -4  -8  -3  -6  -7  -2  -8  -3  -7  13  -2  -9  -7  -8  -6 -10
+Y  -5  -6  -2  -6  -1  -6  -6  -8  -1  -3  -3  -6  -6   4  -8  -4  -4  -2   9  -4  -4  -6  -4 -10
+V   0  -4  -4  -4  -3  -4  -3  -3  -4   3   0  -5   1  -4  -3  -3  -1  -9  -4   6  -4  -3  -2 -10
+B  -1  -3   4   5  -7   0   2  -1   1  -3  -5   0  -5  -6  -3   0  -1  -7  -4  -4   4   2  -2 -10
+Z  -1  -1   0   3  -8   5   5  -2   1  -3  -4  -1  -3  -8  -2  -2  -2  -8  -6  -3   2   5  -2 -10
+X  -1  -2  -1  -2  -5  -2  -2  -2  -2  -2  -3  -2  -2  -4  -2  -1  -1  -6  -4  -2  -2  -2  -2 -10
+* -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10   1

biotite/sequence/align/matrix_data/PB.license

@@ -0,0 +1,21 @@
+The MIT License (MIT)
+
+Copyright (c) 2013 Poulain, A. G. de Brevern
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

biotite/sequence/align/matrix_data/PB.mat

@@ -0,0 +1,18 @@
+# PB substitution matrix, adapted from PBxplore
+   a     b     c     d     e     f     g     h     i     j     k     l     m     n     o     p
+a  516   -59   113  -105  -411  -177   -27  -361    47  -103  -644  -259  -599  -372  -124   -83
+b  -59   541  -146  -210  -155  -310   -97    90   182  -128   -30    29  -745  -242  -165    22
+c  113  -146   360   -14  -333  -240    49  -438  -269  -282  -688  -682  -608  -455  -147     6
+d -105  -210   -14   221     5  -131  -349  -278  -253  -173  -585  -670 -1573 -1048  -691  -497
+e -411  -155  -333     5   520   185   186   138  -378   -70  -112  -514 -1136  -469  -617  -632
+f -177  -310  -240  -131   185   459   -99   -45  -445    83  -214   -88  -547  -629  -406  -552
+g  -27   -97    49  -349   186   -99   665   -99   -89  -118  -409  -138  -124   172   128   254
+h -361    90  -438  -278   138   -45   -99   632  -205   316   192  -108  -712  -359    95  -399
+i   47   182  -269  -253  -378  -445   -89  -205   696   186     8    15  -709  -269  -169   226
+j -103  -128  -282  -173   -70    83  -118   316   186   768   196     5  -398  -340  -117  -104
+k -644   -30  -688  -585  -112  -214  -409   192     8   196   568   -65  -270  -231  -471  -382
+l -259    29  -682  -670  -514   -88  -138  -108    15     5   -65   533  -131     8   -11  -316
+m -599  -745  -608 -1573 -1136  -547  -124  -712  -709  -398  -270  -131   241    -4  -190  -155
+n -372  -242  -455 -1048  -469  -629   172  -359  -269  -340  -231     8    -4   703    88   146
+o -124  -165  -147  -691  -617  -406   128    95  -169  -117  -471   -11  -190    88   716    58
+p  -83    22     6  -497  -632  -552   254  -399   226  -104  -382  -316  -155   146    58   609

biotite/sequence/align/matrix_data/RBLOSUM52_5.0.mat

@@ -0,0 +1,25 @@
+   A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V  B  Z  X  *
+A  5 -2 -1 -2  0 -1 -1  0 -2 -2 -2 -1 -1 -3 -1  1  0 -3 -2  0 -2 -1 -1 -5
+R -2  7  0 -2 -4  1  0 -3  0 -3 -3  3 -2 -4 -3 -1 -1 -2 -2 -3 -1  0 -1 -5
+N -1  0  7  2 -2  0  0  0  1 -3 -3  0 -2 -3 -2  1  0 -3 -2 -3  4  0 -1 -5
+D -2 -2  2  8 -4  0  2 -2  0 -4 -4  0 -3 -5 -2  0 -1 -4 -3 -4  5  2 -1 -5
+C  0 -4 -2 -4 13 -3 -4 -3 -2 -2 -2 -4 -1 -2 -3 -1 -1 -3 -2 -1 -3 -4 -2 -5
+Q -1  1  0  0 -3  7  2 -2  1 -3 -2  2 -1 -4 -1  0 -1 -2 -1 -3  0  4 -1 -5
+E -1  0  0  2 -4  2  7 -3  0 -4 -3  1 -2 -4 -1 -1 -1 -3 -2 -3  1  5 -1 -5
+G  0 -3  0 -2 -3 -2 -3  8 -2 -4 -5 -2 -4 -4 -2  0 -2 -3 -4 -4 -1 -3 -2 -5
+H -2  0  1  0 -2  1  0 -2 10 -4 -2  0 -2 -2 -3 -1 -2 -1  2 -3  0  0 -1 -5
+I -2 -3 -3 -4 -2 -3 -4 -4 -4  6  2 -3  1  0 -3 -3 -1 -2 -1  4 -4 -3 -1 -5
+L -2 -3 -3 -4 -2 -2 -3 -5 -2  2  5 -3  3  1 -4 -3 -2 -1 -1  1 -4 -3 -1 -5
+K -1  3  0  0 -4  2  1 -2  0 -3 -3  6 -2 -4 -2 -1 -1 -3 -2 -3  0  1 -1 -5
+M -1 -2 -2 -3 -1 -1 -2 -4 -2  1  3 -2  7  1 -3 -2 -1 -2 -1  1 -3 -2 -1 -5
+F -3 -4 -3 -5 -2 -4 -4 -4 -2  0  1 -4  1  8 -4 -3 -2  2  4 -1 -4 -4 -2 -5
+P -1 -3 -2 -2 -3 -1 -1 -2 -3 -3 -4 -2 -3 -4 10 -1 -1 -3 -3 -3 -2 -1 -2 -5
+S  1 -1  1  0 -1  0 -1  0 -1 -3 -3 -1 -2 -3 -1  5  2 -4 -2 -2  0 -1 -1 -5
+T  0 -1  0 -1 -1 -1 -1 -2 -2 -1 -2 -1 -1 -2 -1  2  6 -3 -2  0 -1 -1 -1 -5
+W -3 -2 -3 -4 -3 -2 -3 -3 -1 -2 -1 -3 -2  2 -3 -4 -3 15  3 -3 -3 -3 -2 -5
+Y -2 -2 -2 -3 -2 -1 -2 -4  2 -1 -1 -2 -1  4 -3 -2 -2  3  9 -1 -2 -2 -1 -5
+V  0 -3 -3 -4 -1 -3 -3 -4 -3  4  1 -3  1 -1 -3 -2  0 -3 -1  5 -4 -3 -1 -5
+B -2 -1  4  5 -3  0  1 -1  0 -4 -4  0 -3 -4 -2  0 -1 -3 -2 -4  5  1 -1 -5
+Z -1  0  0  2 -4  4  5 -3  0 -3 -3  1 -2 -4 -1 -1 -1 -3 -2 -3  1  4 -1 -5
+X -1 -1 -1 -1 -2 -1 -1 -2 -1 -1 -1 -1 -1 -2 -2 -1 -1 -2 -1 -1 -1 -1 -1 -5
+* -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5  1

biotite/sequence/align/matrix_data/RBLOSUM59_13p.mat

@@ -0,0 +1,25 @@
+   A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V  B  Z  X  *
+A  5 -1 -1 -1 -2 -1 -1  1 -2 -1 -1 -1  0 -2 -1  1  0 -2 -2  0 -1 -1  0 -5
+R -1  7  0 -1 -4  2  1 -2  0 -2 -2  3 -1 -3 -1 -1  0 -2 -2 -2  0  1 -1 -5
+N -1  0  7  2 -3  1  0  0  0 -2 -3  0 -2 -2 -1  1  0 -2 -2 -2  4  0  0 -5
+D -1 -1  2  8 -4  1  3 -1 -1 -3 -4  0 -3 -3  0  0 -1 -3 -3 -3  6  2 -1 -5
+C -2 -4 -3 -4 16 -3 -4 -4 -3 -3 -3 -4 -3 -1 -3 -2 -3 -3 -3 -2 -3 -4 -3 -5
+Q -1  2  1  1 -3  5  2 -2  0 -2 -2  2  0 -2  0  0  0 -1 -2 -2  1  3  0 -5
+E -1  1  0  3 -4  2  6 -2 -1 -3 -3  1 -2 -3  0  0  0 -2 -2 -2  2  5 -1 -5
+G  1 -2  0 -1 -4 -2 -2  9 -2 -4 -4 -2 -3 -3 -1  0 -2 -3 -4 -3  0 -2 -1 -5
+H -2  0  0 -1 -3  0 -1 -2 12 -4 -3  0 -2 -2 -2 -1 -2 -2  0 -3  0 -1 -1 -5
+I -1 -2 -2 -3 -3 -2 -3 -4 -4  6  3 -3  2  1 -2 -2 -1 -1 -1  4 -3 -3 -1 -5
+L -1 -2 -3 -4 -3 -2 -3 -4 -3  3  6 -3  3  1 -3 -3 -2  0 -1  1 -3 -2 -1 -5
+K -1  3  0  0 -4  2  1 -2  0 -3 -3  6 -1 -3 -1  0  0 -2 -2 -2  0  1 -1 -5
+M  0 -1 -2 -3 -3  0 -2 -3 -2  2  3 -1  7  1 -2 -1 -1  0 -1  1 -2 -1  0 -5
+F -2 -3 -2 -3 -1 -2 -3 -3 -2  1  1 -3  1  9 -2 -2 -2  3  4  0 -3 -3 -1 -5
+P -1 -1 -1  0 -3  0  0 -1 -2 -2 -3 -1 -2 -2 10  0  0 -2 -2 -2 -1  0 -1 -5
+S  1 -1  1  0 -2  0  0  0 -1 -2 -3  0 -1 -2  0  4  2 -2 -2 -1  1  0  0 -5
+T  0  0  0 -1 -3  0  0 -2 -2 -1 -2  0 -1 -2  0  2  5 -1 -2  0  0  0  0 -5
+W -2 -2 -2 -3 -3 -1 -2 -3 -2 -1  0 -2  0  3 -2 -2 -1 15  4 -1 -2 -2 -1 -5
+Y -2 -2 -2 -3 -3 -2 -2 -4  0 -1 -1 -2 -1  4 -2 -2 -2  4 11 -1 -2 -2 -1 -5
+V  0 -2 -2 -3 -2 -2 -2 -3 -3  4  1 -2  1  0 -2 -1  0 -1 -1  5 -2 -2  0 -5
+B -1  0  4  6 -3  1  2  0  0 -3 -3  0 -2 -3 -1  1  0 -2 -2 -2  5  2 -1 -5
+Z -1  1  0  2 -4  3  5 -2 -1 -3 -2  1 -1 -3  0  0  0 -2 -2 -2  2  4  0 -5
+X  0 -1  0 -1 -3  0 -1 -1 -1 -1 -1 -1  0 -1 -1  0  0 -1 -1  0 -1  0 -1 -5
+* -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5  1

biotite/sequence/align/matrix_data/RBLOSUM59_14.3.mat

@@ -0,0 +1,25 @@
+   A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V  B  Z  X  *
+A  5 -1 -2 -2  1 -1 -1  0 -1 -1 -1 -2  0 -2 -1  1  0 -2 -2  0 -2 -1  0 -5
+R -1  7  0  0 -3  2  1 -2  1 -3 -3  4 -2 -3 -1 -1 -1 -2 -2 -3  0  2 -1 -5
+N -2  0  7  2 -1  1  0  1  1 -3 -3  1 -2 -3 -1  1  0 -2 -2 -2  5  0  0 -5
+D -2  0  2  8 -2  1  3  0  0 -4 -4  0 -3 -4  0  0 -1 -3 -3 -3  6  3 -1 -5
+C  1 -3 -1 -2 16 -2 -3 -1 -1  0 -1 -3  0  0 -2  0  0 -1 -1  1 -2 -3 -1 -5
+Q -1  2  1  1 -2  6  3 -1  1 -3 -2  2 -1 -3 -1  0  0 -2 -2 -2  1  4  0 -5
+E -1  1  0  3 -3  3  7 -2  0 -3 -3  2 -3 -4 -1 -1 -1 -3 -3 -3  2  6 -1 -5
+G  0 -2  1  0 -1 -1 -2  9 -1 -4 -4 -2 -3 -3 -1  0 -2 -2 -3 -3  0 -2 -1 -5
+H -1  1  1  0 -1  1  0 -1 11 -3 -2  0 -1 -1 -1  0 -1  0  2 -2  1  1  0 -5
+I -1 -3 -3 -4  0 -3 -3 -4 -3  6  3 -3  2  1 -3 -3 -1 -1 -1  4 -3 -3 -1 -5
+L -1 -3 -3 -4 -1 -2 -3 -4 -2  3  6 -3  3  2 -3 -3 -2  1  0  2 -4 -3 -1 -5
+K -2  4  1  0 -3  2  2 -2  0 -3 -3  8 -2 -4 -1 -1 -1 -3 -3 -3  1  2 -1 -5
+M  0 -2 -2 -3  0 -1 -3 -3 -1  2  3 -2  7  2 -3 -2  0  1  0  1 -3 -2  0 -5
+F -2 -3 -3 -4  0 -3 -4 -3 -1  1  2 -4  2  9 -3 -3 -2  4  4  0 -3 -4 -1 -5
+P -1 -1 -1  0 -2 -1 -1 -1 -1 -3 -3 -1 -3 -3 12  0 -1 -2 -3 -2  0 -1 -1 -5
+S  1 -1  1  0  0  0 -1  0  0 -3 -3 -1 -2 -3  0  5  2 -2 -2 -2  1 -1  0 -5
+T  0 -1  0 -1  0  0 -1 -2 -1 -1 -2 -1  0 -2 -1  2  6 -2 -2  0  0 -1  0 -5
+W -2 -2 -2 -3 -1 -2 -3 -2  0 -1  1 -3  1  4 -2 -2 -2 17  4 -1 -2 -2 -1 -5
+Y -2 -2 -2 -3 -1 -2 -3 -3  2 -1  0 -3  0  4 -3 -2 -2  4 12 -1 -2 -2 -1 -5
+V  0 -3 -2 -3  1 -2 -3 -3 -2  4  2 -3  1  0 -2 -2  0 -1 -1  5 -3 -3 -1 -5
+B -2  0  5  6 -2  1  2  0  1 -3 -4  1 -3 -3  0  1  0 -2 -2 -3  5  3 -1 -5
+Z -1  2  0  3 -3  4  6 -2  1 -3 -3  2 -2 -4 -1 -1 -1 -2 -2 -3  3  5 -1 -5
+X  0 -1  0 -1 -1  0 -1 -1  0 -1 -1 -1  0 -1 -1  0  0 -1 -1 -1 -1 -1 -1 -5
+* -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5  1

biotite/sequence/align/matrix_data/RBLOSUM64_5.0.mat

@@ -0,0 +1,25 @@
+   A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V  B  Z  X  *
+A  4 -2 -1 -2 -1 -1 -1  0 -2 -1 -2 -1 -1 -2 -1  1  0 -3 -2  0 -2 -1 -1 -5
+R -2  5  0 -2 -3  1  0 -2  0 -3 -2  2 -2 -3 -2 -1 -1 -2 -2 -3 -1  0 -1 -5
+N -1  0  6  1 -3  0  0 -1  1 -3 -3  0 -2 -3 -2  0  0 -3 -2 -3  3  0 -1 -5
+D -2 -2  1  6 -3  0  2 -2 -1 -3 -3 -1 -3 -3 -2  0 -1 -4 -3 -3  4  1 -1 -5
+C -1 -3 -3 -3  9 -3 -4 -3 -2 -1 -1 -3 -1 -2 -3 -1 -1 -3 -2 -1 -3 -3 -2 -5
+Q -1  1  0  0 -3  5  2 -2  1 -3 -2  1  0 -3 -1  0  0 -2 -2 -2  0  3 -1 -5
+E -1  0  0  2 -4  2  5 -2  0 -3 -3  1 -2 -3 -1  0 -1 -3 -2 -2  1  4 -1 -5
+G  0 -2 -1 -2 -3 -2 -2  6 -2 -4 -4 -2 -3 -3 -2 -1 -2 -2 -3 -3 -1 -2 -2 -5
+H -2  0  1 -1 -2  1  0 -2  7 -3 -3 -1 -1 -1 -2 -1 -2 -1  1 -3  0  0 -1 -5
+I -1 -3 -3 -3 -1 -3 -3 -4 -3  4  2 -3  1  0 -3 -2 -1 -2 -1  2 -3 -3 -1 -5
+L -2 -2 -3 -3 -1 -2 -3 -4 -3  2  4 -2  2  1 -3 -2 -1 -1 -1  1 -3 -2 -1 -5
+K -1  2  0 -1 -3  1  1 -2 -1 -3 -2  5 -1 -3 -1  0 -1 -3 -2 -2  0  1 -1 -5
+M -1 -2 -2 -3 -1  0 -2 -3 -1  1  2 -1  6  0 -2 -1 -1 -2 -1  0 -2 -1 -1 -5
+F -2 -3 -3 -3 -2 -3 -3 -3 -1  0  1 -3  0  6 -3 -2 -2  1  3 -1 -3 -3 -1 -5
+P -1 -2 -2 -2 -3 -1 -1 -2 -2 -3 -3 -1 -2 -3  7 -1 -1 -3 -3 -2 -2 -1 -2 -5
+S  1 -1  0  0 -1  0  0 -1 -1 -2 -2  0 -1 -2 -1  4  1 -3 -2 -2  0  0 -1 -5
+T  0 -1  0 -1 -1  0 -1 -2 -2 -1 -1 -1 -1 -2 -1  1  5 -3 -2  0 -1 -1 -1 -5
+W -3 -2 -3 -4 -3 -2 -3 -2 -1 -2 -1 -3 -2  1 -3 -3 -3 11  2 -3 -3 -3 -2 -5
+Y -2 -2 -2 -3 -2 -2 -2 -3  1 -1 -1 -2 -1  3 -3 -2 -2  2  7 -1 -2 -2 -1 -5
+V  0 -3 -3 -3 -1 -2 -2 -3 -3  2  1 -2  0 -1 -2 -2  0 -3 -1  4 -3 -2 -1 -5
+B -2 -1  3  4 -3  0  1 -1  0 -3 -3  0 -2 -3 -2  0 -1 -3 -2 -3  4  0 -1 -5
+Z -1  0  0  1 -3  3  4 -2  0 -3 -2  1 -1 -3 -1  0 -1 -3 -2 -2  0  3 -1 -5
+X -1 -1 -1 -1 -2 -1 -1 -2 -1 -1 -1 -1 -1 -1 -2 -1 -1 -2 -1 -1 -1 -1 -1 -5
+* -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5  1

biotite/sequence/align/matrix_data/RBLOSUM69_13p.mat

@@ -0,0 +1,25 @@
+   A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V  B  Z  X  *
+A  5 -1 -1 -2 -1 -1 -1  0 -2 -1 -1 -1  0 -2 -1  1  0 -2 -2  0 -2 -1  0 -5
+R -1  6  0 -1 -3  1  1 -2  0 -2 -2  3 -1 -3 -1 -1 -1 -1 -2 -2  0  1 -1 -5
+N -1  0  7  2 -2  0  0  0  1 -3 -3  0 -2 -2 -1  1  0 -2 -1 -2  4  0 -1 -5
+D -2 -1  2  7 -3  1  2 -1 -1 -4 -3  0 -3 -3 -1  0 -1 -3 -3 -3  5  2 -1 -5
+C -1 -3 -2 -3 12 -3 -4 -3 -2 -2 -2 -3 -2 -1 -3 -2 -2 -3 -2 -2 -3 -3 -2 -5
+Q -1  1  0  1 -3  5  2 -2  0 -2 -2  1  0 -2 -1  0  0 -1 -1 -2  1  3  0 -5
+E -1  1  0  2 -4  2  6 -2 -1 -3 -3  1 -2 -3  0 -1 -1 -2 -2 -2  1  4 -1 -5
+G  0 -2  0 -1 -3 -2 -2  7 -2 -4 -4 -2 -3 -3 -2  0 -2 -3 -3 -3 -1 -2 -1 -5
+H -2  0  1 -1 -2  0 -1 -2 10 -3 -3  0 -2 -2 -2 -1 -1 -1  1 -3  0  0 -1 -5
+I -1 -2 -3 -4 -2 -2 -3 -4 -3  5  2 -2  2  0 -3 -2 -1 -1 -1  3 -3 -3 -1 -5
+L -1 -2 -3 -3 -2 -2 -3 -4 -3  2  5 -2  3  1 -3 -3 -2  0 -1  1 -3 -2 -1 -5
+K -1  3  0  0 -3  1  1 -2  0 -2 -2  6 -1 -3 -1 -1  0 -2 -2 -2  0  1 -1 -5
+M  0 -1 -2 -3 -2  0 -2 -3 -2  2  3 -1  6  1 -2 -1 -1  0 -1  1 -2 -1  0 -5
+F -2 -3 -2 -3 -1 -2 -3 -3 -2  0  1 -3  1  8 -2 -2 -2  2  3  0 -3 -3 -1 -5
+P -1 -1 -1 -1 -3 -1  0 -2 -2 -3 -3 -1 -2 -2  9  0 -1 -2 -2 -2 -1 -1 -1 -5
+S  1 -1  1  0 -2  0 -1  0 -1 -2 -3 -1 -1 -2  0  4  2 -2 -2 -1  0  0  0 -5
+T  0 -1  0 -1 -2  0 -1 -2 -1 -1 -2  0 -1 -2 -1  2  5 -1 -2  0  0  0  0 -5
+W -2 -1 -2 -3 -3 -1 -2 -3 -1 -1  0 -2  0  2 -2 -2 -1 13  3 -2 -2 -2 -1 -5
+Y -2 -2 -1 -3 -2 -1 -2 -3  1 -1 -1 -2 -1  3 -2 -2 -2  3  9 -1 -2 -2 -1 -5
+V  0 -2 -2 -3 -2 -2 -2 -3 -3  3  1 -2  1  0 -2 -1  0 -2 -1  4 -3 -2 -1 -5
+B -2  0  4  5 -3  1  1 -1  0 -3 -3  0 -2 -3 -1  0  0 -2 -2 -3  4  1 -1 -5
+Z -1  1  0  2 -3  3  4 -2  0 -3 -2  1 -1 -3 -1  0  0 -2 -2 -2  1  4 -1 -5
+X  0 -1 -1 -1 -2  0 -1 -1 -1 -1 -1 -1  0 -1 -1  0  0 -1 -1 -1 -1 -1 -1 -5
+* -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5  1

biotite/sequence/align/matrix_data/RBLOSUM69_14.3.mat

@@ -0,0 +1,25 @@
+   A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V  B  Z  X  *
+A  5 -1 -2 -2  1 -1 -1  0 -1 -2 -2 -2 -1 -2 -1  1  0 -2 -3 -1 -2 -1 -1 -5
+R -1  7  0  0 -3  2  1 -2  1 -3 -3  3 -2 -3 -1 -1 -1 -2 -2 -3  0  1 -1 -5
+N -2  0  8  2 -1  1  0  1  1 -3 -3  0 -2 -3 -1  1  0 -2 -2 -2  5  0 -1 -5
+D -2  0  2  9 -3  1  3 -1  0 -4 -4  0 -3 -4  0  0 -1 -3 -3 -4  6  3 -1 -5
+C  1 -3 -1 -3 14 -3 -3 -2 -1 -1 -1 -3  0 -1 -3  0  0 -1 -2  1 -2 -3 -1 -5
+Q -1  2  1  1 -3  6  3 -2  1 -3 -2  2 -1 -3 -1  0 -1 -2 -2 -3  1  4  0 -5
+E -1  1  0  3 -3  3  8 -3  0 -4 -4  1 -3 -4 -1 -1 -1 -3 -3 -3  2  6 -1 -5
+G  0 -2  1 -1 -2 -2 -3  9 -1 -5 -4 -2 -3 -3 -1  0 -2 -2 -4 -4  0 -2 -1 -5
+H -1  1  1  0 -1  1  0 -1 11 -3 -2  0 -1 -1 -2 -1 -1  0  2 -3  1  0 -1 -5
+I -2 -3 -3 -4 -1 -3 -4 -5 -3  6  3 -4  2  1 -3 -3 -1 -1 -2  4 -3 -3 -1 -5
+L -2 -3 -3 -4 -1 -2 -4 -4 -2  3  6 -3  3  2 -3 -3 -2  1  0  1 -4 -3 -1 -5
+K -2  3  0  0 -3  2  1 -2  0 -4 -3  8 -2 -4 -1 -1 -1 -3 -3 -3  0  2 -1 -5
+M -1 -2 -2 -3  0 -1 -3 -3 -1  2  3 -2  7  2 -3 -2 -1  1  0  1 -3 -2 -1 -5
+F -2 -3 -3 -4 -1 -3 -4 -3 -1  1  2 -4  2  9 -3 -3 -2  4  4  0 -4 -4 -1 -5
+P -1 -1 -1  0 -3 -1 -1 -1 -2 -3 -3 -1 -3 -3 12  0 -1 -2 -4 -3 -1 -1 -1 -5
+S  1 -1  1  0  0  0 -1  0 -1 -3 -3 -1 -2 -3  0  6  3 -2 -3 -2  0 -1 -1 -5
+T  0 -1  0 -1  0 -1 -1 -2 -1 -1 -2 -1 -1 -2 -1  3  6 -2 -2  0 -1 -1  0 -5
+W -2 -2 -2 -3 -1 -2 -3 -2  0 -1  1 -3  1  4 -2 -2 -2 15  4 -1 -3 -2 -1 -5
+Y -3 -2 -2 -3 -2 -2 -3 -4  2 -2  0 -3  0  4 -4 -3 -2  4 12 -2 -3 -3 -1 -5
+V -1 -3 -2 -4  1 -3 -3 -4 -3  4  1 -3  1  0 -3 -2  0 -1 -2  5 -3 -3 -1 -5
+B -2  0  5  6 -2  1  2  0  1 -3 -4  0 -3 -4 -1  0 -1 -3 -3 -3  5  2 -1 -5
+Z -1  1  0  3 -3  4  6 -2  0 -3 -3  2 -2 -4 -1 -1 -1 -2 -3 -3  2  5 -1 -5
+X -1 -1 -1 -1 -1  0 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1  0 -1 -1 -1 -1 -1 -1 -5
+* -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5  1