Merge branch 'develop' into features/JAL-250_hideredundantseqs

[jalview.git] / resources / scoreModel / pam250.scm

diff --git a/resources/scoreModel/pam250.scm b/resources/scoreModel/pam250.scm
new file mode 100644 (file)
index 0000000..898c723
--- /dev/null
+++ b/resources/scoreModel/pam250.scm
@@ -0,0 +1,32 @@
+ScoreMatrix PAM250
+#
+# The PAM250 substitution matrix
+# The first line declares a ScoreMatrix with the name PAM250 (shown in menus)
+# Scores are not case sensitive, unless column(s) are provided for lower case characters
+# Values may be integer or floating point, delimited by tab, space, comma or combinations
+#
+        A       R       N       D       C       Q       E       G       H       I       L       K       M       F       P       S       T       W       Y       V       B       Z       X       *
+A       2      -2       0       0      -2       0       0       1      -1      -1      -2      -1      -1      -3       1       1       1      -6      -3       0       0       0       0      -8
+R      -2       6       0      -1      -4       1      -1      -3       2      -2      -3       3       0      -4       0       0      -1       2      -4      -2      -1       0      -1      -8
+N       0       0       2       2      -4       1       1       0       2      -2      -3       1      -2      -3       0       1       0      -4      -2      -2       2       1       0      -8
+D       0      -1       2       4      -5       2       3       1       1      -2      -4       0      -3      -6      -1       0       0      -7      -4      -2       3       3      -1      -8
+C      -2      -4      -4      -5      12      -5      -5      -3      -3      -2      -6      -5      -5      -4      -3       0      -2      -8       0      -2      -4      -5      -3      -8
+Q       0       1       1       2      -5       4       2      -1       3      -2      -2       1      -1      -5       0      -1      -1      -5      -4      -2       1       3      -1      -8
+E       0      -1       1       3      -5       2       4       0       1      -2      -3       0      -2      -5      -1       0       0      -7      -4      -2       3       3      -1      -8
+G       1      -3       0       1      -3      -1       0       5      -2      -3      -4      -2      -3      -5       0       1       0      -7      -5      -1       0       0      -1      -8
+H      -1       2       2       1      -3       3       1      -2       6      -2      -2       0      -2      -2       0      -1      -1      -3       0      -2       1       2      -1      -8
+I      -1      -2      -2      -2      -2      -2      -2      -3      -2       5       2      -2       2       1      -2      -1       0      -5      -1       4      -2      -2      -1      -8
+L      -2      -3      -3      -4      -6      -2      -3      -4      -2       2       6      -3       4       2      -3      -3      -2      -2      -1       2      -3      -3      -1      -8
+K      -1       3       1       0      -5       1       0      -2       0      -2      -3       5       0      -5      -1       0       0      -3      -4      -2       1       0      -1      -8
+M      -1       0      -2      -3      -5      -1      -2      -3      -2       2       4       0       6       0      -2      -2      -1      -4      -2       2      -2      -2      -1      -8
+F      -3      -4      -3      -6      -4      -5      -5      -5      -2       1       2      -5       0      9       -5      -3      -3       0       7      -1      -4      -5      -2      -8
+P       1       0       0      -1      -3       0      -1       0       0      -2      -3      -1      -2      -5       6       1       0      -6      -5      -1      -1       0      -1      -8
+S       1       0       1       0       0      -1       0       1      -1      -1      -3       0      -2      -3       1       2       1      -2      -3      -1       0       0       0      -8
+T       1      -1       0       0      -2      -1       0       0      -1       0      -2       0      -1      -3       0       1       3      -5      -3       0       0      -1       0      -8
+W      -6       2      -4      -7      -8      -5      -7      -7      -3      -5      -2      -3      -4       0      -6      -2      -5      17       0      -6      -5      -6      -4      -8
+Y      -3      -4      -2      -4       0      -4      -4      -5       0      -1      -1      -4      -2       7      -5      -3      -3       0      10      -2      -3      -4      -2      -8
+V       0      -2      -2      -2      -2      -2      -2      -1      -2       4       2      -2       2      -1      -1      -1       0      -6      -2       4      -2      -2      -1      -8
+B       0      -1       2       3      -4       1       3       0       1      -2      -3       1      -2      -4      -1       0       0      -5      -3      -2       3       2      -1      -8
+Z       0       0       1       3      -5       3       3       0       2      -2      -3       0      -2      -5       0       0      -1      -6      -4      -2       2       3      -1      -8
+X       0      -1       0      -1      -3      -1      -1      -1      -1      -1      -1      -1      -1      -2      -1       0       0      -4      -2      -1      -1      -1      -1      -8
+*      -8      -8      -8      -8      -8      -8      -8      -8      -8      -8      -8      -8      -8      -8      -8      -8      -8      -8      -8      -8      -8      -8      -8       1