X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=resources%2FscoreModel%2Fpam250.scm;fp=resources%2FscoreModel%2Fpam250.scm;h=898c723bbf7a8855270f2126aaec112135982e0e;hb=f063821ed0be9c1581af74643a1aa5798731af65;hp=0000000000000000000000000000000000000000;hpb=fd18e2c73cd015d4e38ad91da0e5d7532ff0ef42;p=jalview.git

diff --git a/resources/scoreModel/pam250.scm b/resources/scoreModel/pam250.scm
new file mode 100644
index 0000000..898c723
--- /dev/null
+++ b/resources/scoreModel/pam250.scm
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+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