X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Fscorematrices.html;h=5fbbc194f2dde467cf88aad0e748c9d188dd40c7;hb=88141010d441b5fa5fcf43bb3dcbecbbc1721139;hp=5c4a498f781ac8e00391ab57519e7bf90d9bca42;hpb=e5cbd35e13f46ae1d59a08b0af1086677418141d;p=jalview.git
diff --git a/help/html/calculations/scorematrices.html b/help/html/calculations/scorematrices.html
index 5c4a498..5fbbc19 100644
--- a/help/html/calculations/scorematrices.html
+++ b/help/html/calculations/scorematrices.html
@@ -1,7 +1,7 @@
-
+
-
BLOSUM62
-
- | A | B | C | D | E | F | G | H | I | K | L | M | N | P | Q | R | S | T | U | V | W | X | Y | Z |
-A | 4 | -2 | 0 | -2 | -1 | -2 | 0 | -2 | -1 | -1 | -1 | -1 | -2 | -1 | -1 | -1 | 1 | 0 | 0 | 0 | -3 | 0 | -2 | -1 |
-B | -2 | 4 | -3 | 4 | 1 | -3 | -1 | 0 | -3 | 0 | -4 | -3 | 3 | -2 | 0 | -1 | 0 | -1 | -1 | -3 | -4 | -1 | -3 | 1 |
-C | 0 | -3 | 9 | -3 | -4 | -2 | -3 | -3 | -1 | -3 | -1 | -1 | -3 | -3 | -3 | 3 | -1 | -1 | -2 | -1 | -2 | -2 | -2 | -3 |
-D | -2 | 4 | -3 | 6 | 2 | -3 | -1 | -1 | -3 | -1 | -4 | -3 | 1 | -1 | 0 | -2 | 0 | -1 | -1 | -3 | -4 | -1 | -3 | 1 |
-E | -1 | 1 | -4 | 2 | 5 | -3 | -2 | 0 | -3 | 1 | -3 | -2 | 0 | -1 | 2 | 0 | 0 | -1 | -1 | -2 | -3 | -1 | -2 | 4 |
-F | -2 | -3 | -2 | -3 | -3 | 6 | -3 | -1 | 0 | -3 | 0 | 0 | -3 | -4 | -3 | -3 | -2 | -2 | -1 | -1 | 1 | -1 | 3 | -3 |
-G | 0 | -1 | -3 | -1 | -2 | -3 | 6 | -2 | -4 | -2 | -4 | -3 | 0 | -2 | -2 | -2 | 0 | -2 | -1 | -3 | -2 | -1 | -3 | -2 |
-H | -2 | 0 | -3 | -1 | 0 | -1 | -2 | 8 | -3 | -1 | -3 | -2 | 1 | -2 | 0 | 0 | -1 | -2 | -1 | -3 | -2 | -1 | 2 | 0 |
-I | -1 | -3 | -1 | -3 | -3 | 0 | -4 | -3 | 4 | -3 | 2 | 1 | -3 | -3 | -3 | -3 | -2 | -1 | -1 | 3 | -3 | -1 | -1 | -3 |
-K | -1 | 0 | -3 | -1 | 1 | -3 | -2 | -1 | -3 | 5 | -2 | -1 | 0 | -1 | 1 | 2 | 0 | -1 | -1 | -2 | -3 | -1 | -2 | 1 |
-L | -1 | -4 | -1 | -4 | -3 | 0 | -4 | -3 | 2 | -2 | 4 | 2 | -3 | -3 | -2 | -2 | -2 | -1 | -1 | 1 | -2 | -1 | -1 | -3 |
-M | -1 | -3 | -1 | -3 | -2 | 0 | -3 | -2 | 1 | -1 | 2 | 5 | -2 | -2 | 0 | -1 | -1 | -1 | -1 | 1 | -1 | -1 | -1 | -1 |
-N | -2 | 3 | -3 | 1 | 0 | -3 | 0 | 1 | -3 | 0 | -3 | -2 | 6 | -2 | 0 | 0 | 1 | 0 | -1 | -3 | -4 | -1 | -2 | 0 |
-P | -1 | -2 | -3 | -1 | -1 | -4 | -2 | -2 | -3 | -1 | -3 | -2 | -2 | 7 | -1 | -2 | -1 | -1 | -2 | -2 | -4 | -2 | -3 | -1 |
-Q | -1 | 0 | -3 | 0 | 2 | -3 | -2 | 0 | -3 | 1 | -2 | 0 | 0 | -1 | 5 | 1 | 0 | -1 | -1 | -2 | -2 | -1 | -1 | 3 |
-R | -1 | -1 | -3 | -2 | 0 | -3 | -2 | 0 | -3 | 2 | -2 | -1 | 0 | -2 | 1 | 5 | -1 | -1 | -1 | -3 | -3 | -1 | -2 | 0 |
-S | 1 | 0 | -1 | 0 | 0 | -2 | 0 | -1 | -2 | 0 | -2 | -1 | 1 | -1 | 0 | -1 | 4 | 1 | 0 | -2 | -3 | 0 | -2 | 0 |
-T | 0 | -1 | -1 | -1 | -1 | -2 | -2 | -2 | -1 | -1 | -1 | -1 | 0 | -1 | -1 | -1 | 1 | 5 | 0 | 0 | -2 | 0 | -2 | -1 |
-U | 0 | -1 | -2 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -2 | -1 | -1 | 0 | 0 | -1 | -1 | -2 | -1 | -1 | -1 |
-V | 0 | -3 | -1 | -3 | -2 | -1 | -3 | -3 | 3 | -2 | 1 | 1 | -3 | -2 | -2 | -3 | -2 | 0 | -1 | 4 | -3 | -1 | -1 | -2 |
-W | -3 | -4 | -2 | -4 | -3 | 1 | -2 | -2 | -3 | -3 | -2 | -1 | -4 | -4 | -2 | -3 | -3 | -2 | -2 | -3 | 11 | -2 | 2 | -3 |
-X | 0 | -1 | -2 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -2 | -1 | -1 | 0 | 0 | -1 | -1 | -2 | -1 | -1 | -1 |
-Y | -2 | -3 | -2 | -3 | -2 | 3 | -3 | 2 | -1 | -2 | -1 | -1 | -2 | -3 | -1 | -2 | -2 | -2 | -1 | -1 | 2 | -1 | 7 | -2 |
-Z | -1 | 1 | -3 | 1 | 4 | -3 | -2 | 0 | -3 | 1 | -3 | -1 | 0 | -1 | 3 | 0 | 0 | -1 | -1 | -2 | -3 | -1 | -2 | 4 |
-
-PAM250
-Percentage Accepted Mutation matrix. PAM250 estimates substitutions after 250% of sites have changed (each site can be mutated multple times).
-Jalview 2.8.1 introduced support for PAM250 based PCA and tree calculations.
-
- | A | B | C | D | E | F | G | H | I | K | L | M | N | P | Q | R | S | T | U | V | W | X | Y | Z |
-A | 2 | 0 | -2 | 0 | 0 | -3 | 1 | -1 | -1 | -1 | -2 | -1 | 0 | 1 | 0 | -2 | 1 | 1 | 0 | 0 | -6 | 0 | -3 | 0 |
-B | 0 | 3 | -4 | 3 | 3 | -4 | 0 | 1 | -2 | 1 | -3 | -2 | 2 | -1 | 1 | -1 | 0 | 0 | -1 | -2 | -5 | -1 | -3 | 2 |
-C | -2 | -4 | 12 | -5 | -5 | -4 | -3 | -3 | -2 | -5 | -6 | -5 | -4 | -3 | -5 | -4 | 0 | -2 | -3 | -2 | -8 | -3 | 0 | -5 |
-D | 0 | 3 | -5 | 4 | 3 | -6 | 1 | 1 | -2 | 0 | -4 | -3 | 2 | -1 | 2 | -1 | 0 | 0 | -1 | -2 | -7 | -1 | -4 | 3 |
-E | 0 | 3 | -5 | 3 | 4 | -5 | 0 | 1 | -2 | 0 | -3 | -2 | 1 | -1 | 2 | -1 | 0 | 0 | -1 | -2 | -7 | -1 | -4 | 3 |
-F | -3 | -4 | -4 | -6 | -5 | 9 | -5 | -2 | 1 | -5 | 2 | 0 | -3 | -5 | -5 | -4 | -3 | -3 | -2 | -1 | 0 | -2 | 7 | -5 |
-G | 1 | 0 | -3 | 1 | 0 | -5 | 5 | -2 | -3 | -2 | -4 | -3 | 0 | 0 | -1 | -3 | 1 | 0 | -1 | -1 | -7 | -1 | -5 | 0 |
-H | -1 | 1 | -3 | 1 | 1 | -2 | -2 | 6 | -2 | 0 | -2 | -2 | 2 | 0 | 3 | 2 | -1 | -1 | -1 | -2 | -3 | -1 | 0 | 2 |
-I | -1 | -2 | -2 | -2 | -2 | 1 | -3 | -2 | 5 | -2 | 2 | 2 | -2 | -2 | -2 | -2 | -1 | 0 | -1 | 4 | -5 | -1 | -1 | -2 |
-K | -1 | 1 | -5 | 0 | 0 | -5 | -2 | 0 | -2 | 5 | -3 | 0 | 1 | -1 | 1 | 3 | 0 | 0 | -1 | -2 | -3 | -1 | -4 | 0 |
-L | -2 | -3 | -6 | -4 | -3 | 2 | -4 | -2 | 2 | -3 | 6 | 4 | -3 | -3 | -2 | -3 | -3 | -2 | -1 | 2 | -2 | -1 | -1 | -3 |
-M | -1 | -2 | -5 | -3 | -2 | 0 | -3 | -2 | 2 | 0 | 4 | 6 | -2 | -2 | -1 | 0 | -2 | -1 | -1 | 2 | -4 | -1 | -2 | -2 |
-N | 0 | 2 | -4 | 2 | 1 | -3 | 0 | 2 | -2 | 1 | -3 | -2 | 2 | 0 | 1 | 0 | 1 | 0 | 0 | -2 | -4 | 0 | -2 | 1 |
-P | 1 | -1 | -3 | -1 | -1 | -5 | 0 | 0 | -2 | -1 | -3 | -2 | 0 | 6 | 0 | 0 | 1 | 0 | -1 | -1 | -6 | -1 | -5 | 0 |
-Q | 0 | 1 | -5 | 2 | 2 | -5 | -1 | 3 | -2 | 1 | -2 | -1 | 1 | 0 | 4 | 1 | -1 | -1 | -1 | -2 | -5 | -1 | -4 | 3 |
-R | -2 | -1 | -4 | -1 | -1 | -4 | -3 | 2 | -2 | 3 | -3 | 0 | 0 | 0 | 1 | 6 | 0 | -1 | -1 | -2 | 2 | -1 | -4 | 0 |
-S | 1 | 0 | 0 | 0 | 0 | -3 | 1 | -1 | -1 | 0 | -3 | -2 | 1 | 1 | -1 | 0 | 2 | 1 | 0 | -1 | -2 | 0 | -3 | 0 |
-T | 1 | 0 | -2 | 0 | 0 | -3 | 0 | -1 | 0 | 0 | -2 | -1 | 0 | 0 | -1 | -1 | 1 | 3 | 0 | 0 | -5 | 0 | -3 | -1 |
-U | 0 | -1 | -3 | -1 | -1 | -2 | -1 | -1 | -1 | -1 | -1 | -1 | 0 | -1 | -1 | -1 | 0 | 0 | -1 | -1 | -4 | -1 | -2 | -1 |
-V | 0 | -2 | -2 | -2 | -2 | -1 | -1 | -2 | 4 | -2 | 2 | 2 | -2 | -1 | -2 | -2 | -1 | 0 | -1 | 4 | -6 | -1 | -2 | -2 |
-W | -6 | -5 | -8 | -7 | -7 | 0 | -7 | -3 | -5 | -3 | -2 | -4 | -4 | -6 | -5 | 2 | -2 | -5 | -4 | -6 | 17 | -4 | 0 | -6 |
-X | 0 | -1 | -3 | -1 | -1 | -2 | -1 | -1 | -1 | -1 | -1 | -1 | 0 | -1 | -1 | -1 | 0 | 0 | -1 | -1 | -4 | -1 | -2 | -1 |
-Y | -3 | -3 | 0 | -4 | -4 | 7 | -5 | 0 | -1 | -4 | -1 | -2 | -2 | -5 | -4 | -4 | -3 | -3 | -2 | -2 | 0 | -2 | 10 | -4 |
-Z | 0 | 2 | -5 | 3 | 3 | -5 | 0 | 2 | -2 | 0 | -3 | -2 | 1 | 0 | 3 | 0 | 0 | -1 | -1 | -2 | -6 | -1 | -4 | 3 |
-
+
+ BLOSUM62
+
+
+ |
+ A |
+ B |
+ C |
+ D |
+ E |
+ F |
+ G |
+ H |
+ I |
+ K |
+ L |
+ M |
+ N |
+ P |
+ Q |
+ R |
+ S |
+ T |
+ U |
+ V |
+ W |
+ X |
+ Y |
+ Z |
+
+
+ A |
+ 4 |
+ -2 |
+ 0 |
+ -2 |
+ -1 |
+ -2 |
+ 0 |
+ -2 |
+ -1 |
+ -1 |
+ -1 |
+ -1 |
+ -2 |
+ -1 |
+ -1 |
+ -1 |
+ 1 |
+ 0 |
+ 0 |
+ 0 |
+ -3 |
+ 0 |
+ -2 |
+ -1 |
+
+
+ B |
+ -2 |
+ 4 |
+ -3 |
+ 4 |
+ 1 |
+ -3 |
+ -1 |
+ 0 |
+ -3 |
+ 0 |
+ -4 |
+ -3 |
+ 3 |
+ -2 |
+ 0 |
+ -1 |
+ 0 |
+ -1 |
+ -1 |
+ -3 |
+ -4 |
+ -1 |
+ -3 |
+ 1 |
+
+
+ C |
+ 0 |
+ -3 |
+ 9 |
+ -3 |
+ -4 |
+ -2 |
+ -3 |
+ -3 |
+ -1 |
+ -3 |
+ -1 |
+ -1 |
+ -3 |
+ -3 |
+ -3 |
+ 3 |
+ -1 |
+ -1 |
+ -2 |
+ -1 |
+ -2 |
+ -2 |
+ -2 |
+ -3 |
+
+
+ D |
+ -2 |
+ 4 |
+ -3 |
+ 6 |
+ 2 |
+ -3 |
+ -1 |
+ -1 |
+ -3 |
+ -1 |
+ -4 |
+ -3 |
+ 1 |
+ -1 |
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+ -2 |
+ 0 |
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+ -1 |
+ -3 |
+ -4 |
+ -1 |
+ -3 |
+ 1 |
+
+
+ E |
+ -1 |
+ 1 |
+ -4 |
+ 2 |
+ 5 |
+ -3 |
+ -2 |
+ 0 |
+ -3 |
+ 1 |
+ -3 |
+ -2 |
+ 0 |
+ -1 |
+ 2 |
+ 0 |
+ 0 |
+ -1 |
+ -1 |
+ -2 |
+ -3 |
+ -1 |
+ -2 |
+ 4 |
+
+
+ F |
+ -2 |
+ -3 |
+ -2 |
+ -3 |
+ -3 |
+ 6 |
+ -3 |
+ -1 |
+ 0 |
+ -3 |
+ 0 |
+ 0 |
+ -3 |
+ -4 |
+ -3 |
+ -3 |
+ -2 |
+ -2 |
+ -1 |
+ -1 |
+ 1 |
+ -1 |
+ 3 |
+ -3 |
+
+
+ G |
+ 0 |
+ -1 |
+ -3 |
+ -1 |
+ -2 |
+ -3 |
+ 6 |
+ -2 |
+ -4 |
+ -2 |
+ -4 |
+ -3 |
+ 0 |
+ -2 |
+ -2 |
+ -2 |
+ 0 |
+ -2 |
+ -1 |
+ -3 |
+ -2 |
+ -1 |
+ -3 |
+ -2 |
+
+
+ H |
+ -2 |
+ 0 |
+ -3 |
+ -1 |
+ 0 |
+ -1 |
+ -2 |
+ 8 |
+ -3 |
+ -1 |
+ -3 |
+ -2 |
+ 1 |
+ -2 |
+ 0 |
+ 0 |
+ -1 |
+ -2 |
+ -1 |
+ -3 |
+ -2 |
+ -1 |
+ 2 |
+ 0 |
+
+
+ I |
+ -1 |
+ -3 |
+ -1 |
+ -3 |
+ -3 |
+ 0 |
+ -4 |
+ -3 |
+ 4 |
+ -3 |
+ 2 |
+ 1 |
+ -3 |
+ -3 |
+ -3 |
+ -3 |
+ -2 |
+ -1 |
+ -1 |
+ 3 |
+ -3 |
+ -1 |
+ -1 |
+ -3 |
+
+
+ K |
+ -1 |
+ 0 |
+ -3 |
+ -1 |
+ 1 |
+ -3 |
+ -2 |
+ -1 |
+ -3 |
+ 5 |
+ -2 |
+ -1 |
+ 0 |
+ -1 |
+ 1 |
+ 2 |
+ 0 |
+ -1 |
+ -1 |
+ -2 |
+ -3 |
+ -1 |
+ -2 |
+ 1 |
+
+
+ L |
+ -1 |
+ -4 |
+ -1 |
+ -4 |
+ -3 |
+ 0 |
+ -4 |
+ -3 |
+ 2 |
+ -2 |
+ 4 |
+ 2 |
+ -3 |
+ -3 |
+ -2 |
+ -2 |
+ -2 |
+ -1 |
+ -1 |
+ 1 |
+ -2 |
+ -1 |
+ -1 |
+ -3 |
+
+
+ M |
+ -1 |
+ -3 |
+ -1 |
+ -3 |
+ -2 |
+ 0 |
+ -3 |
+ -2 |
+ 1 |
+ -1 |
+ 2 |
+ 5 |
+ -2 |
+ -2 |
+ 0 |
+ -1 |
+ -1 |
+ -1 |
+ -1 |
+ 1 |
+ -1 |
+ -1 |
+ -1 |
+ -1 |
+
+
+ N |
+ -2 |
+ 3 |
+ -3 |
+ 1 |
+ 0 |
+ -3 |
+ 0 |
+ 1 |
+ -3 |
+ 0 |
+ -3 |
+ -2 |
+ 6 |
+ -2 |
+ 0 |
+ 0 |
+ 1 |
+ 0 |
+ -1 |
+ -3 |
+ -4 |
+ -1 |
+ -2 |
+ 0 |
+
+
+ P |
+ -1 |
+ -2 |
+ -3 |
+ -1 |
+ -1 |
+ -4 |
+ -2 |
+ -2 |
+ -3 |
+ -1 |
+ -3 |
+ -2 |
+ -2 |
+ 7 |
+ -1 |
+ -2 |
+ -1 |
+ -1 |
+ -2 |
+ -2 |
+ -4 |
+ -2 |
+ -3 |
+ -1 |
+
+
+ Q |
+ -1 |
+ 0 |
+ -3 |
+ 0 |
+ 2 |
+ -3 |
+ -2 |
+ 0 |
+ -3 |
+ 1 |
+ -2 |
+ 0 |
+ 0 |
+ -1 |
+ 5 |
+ 1 |
+ 0 |
+ -1 |
+ -1 |
+ -2 |
+ -2 |
+ -1 |
+ -1 |
+ 3 |
+
+
+ R |
+ -1 |
+ -1 |
+ -3 |
+ -2 |
+ 0 |
+ -3 |
+ -2 |
+ 0 |
+ -3 |
+ 2 |
+ -2 |
+ -1 |
+ 0 |
+ -2 |
+ 1 |
+ 5 |
+ -1 |
+ -1 |
+ -1 |
+ -3 |
+ -3 |
+ -1 |
+ -2 |
+ 0 |
+
+
+ S |
+ 1 |
+ 0 |
+ -1 |
+ 0 |
+ 0 |
+ -2 |
+ 0 |
+ -1 |
+ -2 |
+ 0 |
+ -2 |
+ -1 |
+ 1 |
+ -1 |
+ 0 |
+ -1 |
+ 4 |
+ 1 |
+ 0 |
+ -2 |
+ -3 |
+ 0 |
+ -2 |
+ 0 |
+
+
+ T |
+ 0 |
+ -1 |
+ -1 |
+ -1 |
+ -1 |
+ -2 |
+ -2 |
+ -2 |
+ -1 |
+ -1 |
+ -1 |
+ -1 |
+ 0 |
+ -1 |
+ -1 |
+ -1 |
+ 1 |
+ 5 |
+ 0 |
+ 0 |
+ -2 |
+ 0 |
+ -2 |
+ -1 |
+
+
+ U |
+ 0 |
+ -1 |
+ -2 |
+ -1 |
+ -1 |
+ -1 |
+ -1 |
+ -1 |
+ -1 |
+ -1 |
+ -1 |
+ -1 |
+ -1 |
+ -2 |
+ -1 |
+ -1 |
+ 0 |
+ 0 |
+ -1 |
+ -1 |
+ -2 |
+ -1 |
+ -1 |
+ -1 |
+
+
+ V |
+ 0 |
+ -3 |
+ -1 |
+ -3 |
+ -2 |
+ -1 |
+ -3 |
+ -3 |
+ 3 |
+ -2 |
+ 1 |
+ 1 |
+ -3 |
+ -2 |
+ -2 |
+ -3 |
+ -2 |
+ 0 |
+ -1 |
+ 4 |
+ -3 |
+ -1 |
+ -1 |
+ -2 |
+
+
+ W |
+ -3 |
+ -4 |
+ -2 |
+ -4 |
+ -3 |
+ 1 |
+ -2 |
+ -2 |
+ -3 |
+ -3 |
+ -2 |
+ -1 |
+ -4 |
+ -4 |
+ -2 |
+ -3 |
+ -3 |
+ -2 |
+ -2 |
+ -3 |
+ 11 |
+ -2 |
+ 2 |
+ -3 |
+
+
+ X |
+ 0 |
+ -1 |
+ -2 |
+ -1 |
+ -1 |
+ -1 |
+ -1 |
+ -1 |
+ -1 |
+ -1 |
+ -1 |
+ -1 |
+ -1 |
+ -2 |
+ -1 |
+ -1 |
+ 0 |
+ 0 |
+ -1 |
+ -1 |
+ -2 |
+ -1 |
+ -1 |
+ -1 |
+
+
+ Y |
+ -2 |
+ -3 |
+ -2 |
+ -3 |
+ -2 |
+ 3 |
+ -3 |
+ 2 |
+ -1 |
+ -2 |
+ -1 |
+ -1 |
+ -2 |
+ -3 |
+ -1 |
+ -2 |
+ -2 |
+ -2 |
+ -1 |
+ -1 |
+ 2 |
+ -1 |
+ 7 |
+ -2 |
+
+
+ Z |
+ -1 |
+ 1 |
+ -3 |
+ 1 |
+ 4 |
+ -3 |
+ -2 |
+ 0 |
+ -3 |
+ 1 |
+ -3 |
+ -1 |
+ 0 |
+ -1 |
+ 3 |
+ 0 |
+ 0 |
+ -1 |
+ -1 |
+ -2 |
+ -3 |
+ -1 |
+ -2 |
+ 4 |
+
+
+
+ PAM250
Percentage
+ Accepted Mutation matrix. PAM250
+ estimates substitutions after 250% of sites have changed (each
+ site can be mutated multple times).
Jalview 2.8.1
+ introduced support for PAM250 based PCA and tree calculations.
+
+
+ |
+ A |
+ B |
+ C |
+ D |
+ E |
+ F |
+ G |
+ H |
+ I |
+ K |
+ L |
+ M |
+ N |
+ P |
+ Q |
+ R |
+ S |
+ T |
+ U |
+ V |
+ W |
+ X |
+ Y |
+ Z |
+
+
+ A |
+ 2 |
+ 0 |
+ -2 |
+ 0 |
+ 0 |
+ -3 |
+ 1 |
+ -1 |
+ -1 |
+ -1 |
+ -2 |
+ -1 |
+ 0 |
+ 1 |
+ 0 |
+ -2 |
+ 1 |
+ 1 |
+ 0 |
+ 0 |
+ -6 |
+ 0 |
+ -3 |
+ 0 |
+
+
+ B |
+ 0 |
+ 3 |
+ -4 |
+ 3 |
+ 3 |
+ -4 |
+ 0 |
+ 1 |
+ -2 |
+ 1 |
+ -3 |
+ -2 |
+ 2 |
+ -1 |
+ 1 |
+ -1 |
+ 0 |
+ 0 |
+ -1 |
+ -2 |
+ -5 |
+ -1 |
+ -3 |
+ 2 |
+
+
+ C |
+ -2 |
+ -4 |
+ 12 |
+ -5 |
+ -5 |
+ -4 |
+ -3 |
+ -3 |
+ -2 |
+ -5 |
+ -6 |
+ -5 |
+ -4 |
+ -3 |
+ -5 |
+ -4 |
+ 0 |
+ -2 |
+ -3 |
+ -2 |
+ -8 |
+ -3 |
+ 0 |
+ -5 |
+
+
+ D |
+ 0 |
+ 3 |
+ -5 |
+ 4 |
+ 3 |
+ -6 |
+ 1 |
+ 1 |
+ -2 |
+ 0 |
+ -4 |
+ -3 |
+ 2 |
+ -1 |
+ 2 |
+ -1 |
+ 0 |
+ 0 |
+ -1 |
+ -2 |
+ -7 |
+ -1 |
+ -4 |
+ 3 |
+
+
+ E |
+ 0 |
+ 3 |
+ -5 |
+ 3 |
+ 4 |
+ -5 |
+ 0 |
+ 1 |
+ -2 |
+ 0 |
+ -3 |
+ -2 |
+ 1 |
+ -1 |
+ 2 |
+ -1 |
+ 0 |
+ 0 |
+ -1 |
+ -2 |
+ -7 |
+ -1 |
+ -4 |
+ 3 |
+
+
+ F |
+ -3 |
+ -4 |
+ -4 |
+ -6 |
+ -5 |
+ 9 |
+ -5 |
+ -2 |
+ 1 |
+ -5 |
+ 2 |
+ 0 |
+ -3 |
+ -5 |
+ -5 |
+ -4 |
+ -3 |
+ -3 |
+ -2 |
+ -1 |
+ 0 |
+ -2 |
+ 7 |
+ -5 |
+
+
+ G |
+ 1 |
+ 0 |
+ -3 |
+ 1 |
+ 0 |
+ -5 |
+ 5 |
+ -2 |
+ -3 |
+ -2 |
+ -4 |
+ -3 |
+ 0 |
+ 0 |
+ -1 |
+ -3 |
+ 1 |
+ 0 |
+ -1 |
+ -1 |
+ -7 |
+ -1 |
+ -5 |
+ 0 |
+
+
+ H |
+ -1 |
+ 1 |
+ -3 |
+ 1 |
+ 1 |
+ -2 |
+ -2 |
+ 6 |
+ -2 |
+ 0 |
+ -2 |
+ -2 |
+ 2 |
+ 0 |
+ 3 |
+ 2 |
+ -1 |
+ -1 |
+ -1 |
+ -2 |
+ -3 |
+ -1 |
+ 0 |
+ 2 |
+
+
+ I |
+ -1 |
+ -2 |
+ -2 |
+ -2 |
+ -2 |
+ 1 |
+ -3 |
+ -2 |
+ 5 |
+ -2 |
+ 2 |
+ 2 |
+ -2 |
+ -2 |
+ -2 |
+ -2 |
+ -1 |
+ 0 |
+ -1 |
+ 4 |
+ -5 |
+ -1 |
+ -1 |
+ -2 |
+
+
+ K |
+ -1 |
+ 1 |
+ -5 |
+ 0 |
+ 0 |
+ -5 |
+ -2 |
+ 0 |
+ -2 |
+ 5 |
+ -3 |
+ 0 |
+ 1 |
+ -1 |
+ 1 |
+ 3 |
+ 0 |
+ 0 |
+ -1 |
+ -2 |
+ -3 |
+ -1 |
+ -4 |
+ 0 |
+
+
+ L |
+ -2 |
+ -3 |
+ -6 |
+ -4 |
+ -3 |
+ 2 |
+ -4 |
+ -2 |
+ 2 |
+ -3 |
+ 6 |
+ 4 |
+ -3 |
+ -3 |
+ -2 |
+ -3 |
+ -3 |
+ -2 |
+ -1 |
+ 2 |
+ -2 |
+ -1 |
+ -1 |
+ -3 |
+
+
+ M |
+ -1 |
+ -2 |
+ -5 |
+ -3 |
+ -2 |
+ 0 |
+ -3 |
+ -2 |
+ 2 |
+ 0 |
+ 4 |
+ 6 |
+ -2 |
+ -2 |
+ -1 |
+ 0 |
+ -2 |
+ -1 |
+ -1 |
+ 2 |
+ -4 |
+ -1 |
+ -2 |
+ -2 |
+
+
+ N |
+ 0 |
+ 2 |
+ -4 |
+ 2 |
+ 1 |
+ -3 |
+ 0 |
+ 2 |
+ -2 |
+ 1 |
+ -3 |
+ -2 |
+ 2 |
+ 0 |
+ 1 |
+ 0 |
+ 1 |
+ 0 |
+ 0 |
+ -2 |
+ -4 |
+ 0 |
+ -2 |
+ 1 |
+
+
+ P |
+ 1 |
+ -1 |
+ -3 |
+ -1 |
+ -1 |
+ -5 |
+ 0 |
+ 0 |
+ -2 |
+ -1 |
+ -3 |
+ -2 |
+ 0 |
+ 6 |
+ 0 |
+ 0 |
+ 1 |
+ 0 |
+ -1 |
+ -1 |
+ -6 |
+ -1 |
+ -5 |
+ 0 |
+
+
+ Q |
+ 0 |
+ 1 |
+ -5 |
+ 2 |
+ 2 |
+ -5 |
+ -1 |
+ 3 |
+ -2 |
+ 1 |
+ -2 |
+ -1 |
+ 1 |
+ 0 |
+ 4 |
+ 1 |
+ -1 |
+ -1 |
+ -1 |
+ -2 |
+ -5 |
+ -1 |
+ -4 |
+ 3 |
+
+
+ R |
+ -2 |
+ -1 |
+ -4 |
+ -1 |
+ -1 |
+ -4 |
+ -3 |
+ 2 |
+ -2 |
+ 3 |
+ -3 |
+ 0 |
+ 0 |
+ 0 |
+ 1 |
+ 6 |
+ 0 |
+ -1 |
+ -1 |
+ -2 |
+ 2 |
+ -1 |
+ -4 |
+ 0 |
+
+
+ S |
+ 1 |
+ 0 |
+ 0 |
+ 0 |
+ 0 |
+ -3 |
+ 1 |
+ -1 |
+ -1 |
+ 0 |
+ -3 |
+ -2 |
+ 1 |
+ 1 |
+ -1 |
+ 0 |
+ 2 |
+ 1 |
+ 0 |
+ -1 |
+ -2 |
+ 0 |
+ -3 |
+ 0 |
+
+
+ T |
+ 1 |
+ 0 |
+ -2 |
+ 0 |
+ 0 |
+ -3 |
+ 0 |
+ -1 |
+ 0 |
+ 0 |
+ -2 |
+ -1 |
+ 0 |
+ 0 |
+ -1 |
+ -1 |
+ 1 |
+ 3 |
+ 0 |
+ 0 |
+ -5 |
+ 0 |
+ -3 |
+ -1 |
+
+
+ U |
+ 0 |
+ -1 |
+ -3 |
+ -1 |
+ -1 |
+ -2 |
+ -1 |
+ -1 |
+ -1 |
+ -1 |
+ -1 |
+ -1 |
+ 0 |
+ -1 |
+ -1 |
+ -1 |
+ 0 |
+ 0 |
+ -1 |
+ -1 |
+ -4 |
+ -1 |
+ -2 |
+ -1 |
+
+
+ V |
+ 0 |
+ -2 |
+ -2 |
+ -2 |
+ -2 |
+ -1 |
+ -1 |
+ -2 |
+ 4 |
+ -2 |
+ 2 |
+ 2 |
+ -2 |
+ -1 |
+ -2 |
+ -2 |
+ -1 |
+ 0 |
+ -1 |
+ 4 |
+ -6 |
+ -1 |
+ -2 |
+ -2 |
+
+
+ W |
+ -6 |
+ -5 |
+ -8 |
+ -7 |
+ -7 |
+ 0 |
+ -7 |
+ -3 |
+ -5 |
+ -3 |
+ -2 |
+ -4 |
+ -4 |
+ -6 |
+ -5 |
+ 2 |
+ -2 |
+ -5 |
+ -4 |
+ -6 |
+ 17 |
+ -4 |
+ 0 |
+ -6 |
+
+
+ X |
+ 0 |
+ -1 |
+ -3 |
+ -1 |
+ -1 |
+ -2 |
+ -1 |
+ -1 |
+ -1 |
+ -1 |
+ -1 |
+ -1 |
+ 0 |
+ -1 |
+ -1 |
+ -1 |
+ 0 |
+ 0 |
+ -1 |
+ -1 |
+ -4 |
+ -1 |
+ -2 |
+ -1 |
+
+
+ Y |
+ -3 |
+ -3 |
+ 0 |
+ -4 |
+ -4 |
+ 7 |
+ -5 |
+ 0 |
+ -1 |
+ -4 |
+ -1 |
+ -2 |
+ -2 |
+ -5 |
+ -4 |
+ -4 |
+ -3 |
+ -3 |
+ -2 |
+ -2 |
+ 0 |
+ -2 |
+ 10 |
+ -4 |
+
+
+ Z |
+ 0 |
+ 2 |
+ -5 |
+ 3 |
+ 3 |
+ -5 |
+ 0 |
+ 2 |
+ -2 |
+ 0 |
+ -3 |
+ -2 |
+ 1 |
+ 0 |
+ 3 |
+ 0 |
+ 0 |
+ -1 |
+ -1 |
+ -2 |
+ -6 |
+ -1 |
+ -4 |
+ 3 |
+
+
-Simple Nucleotide Substitution
-This is an ad-hoc matrix which, in addition to penalising mutations between the common nucleotides (ACGT), includes T/U equivalence in order to allow both DNA and/or RNA.
-In addition, it encodes weak equivalence between R and Y with AG and CTU, respectively, and N is allowed to match any other base weakly. This matrix also includes I (Inosine) and X (Xanthine), but encodes them to weakly match any of (ACGTU), and unfavourably match each other.
-
- | A | C | G | I | N | R | T | U | X | Y |
-A | 10 | -8 | -8 | 1 | 1 | 1 | -8 | -8 | 1 | -8 |
-C | -8 | 10 | -8 | 1 | 1 | -8 | -8 | -8 | 1 | 1 |
-G | -8 | -8 | 10 | 1 | 1 | 1 | -8 | -8 | 1 | -8 |
-I | 1 | 1 | 1 | 10 | 1 | 0 | 1 | 1 | 0 | 0 |
-N | 1 | 1 | 1 | 1 | 10 | 1 | 1 | 1 | 1 | 1 |
-R | 1 | -8 | 1 | 0 | 1 | 10 | -8 | -8 | 0 | -8 |
-T | -8 | -8 | -8 | 1 | 1 | -8 | 10 | 10 | 1 | 1 |
-U | -8 | -8 | -8 | 1 | 1 | -8 | 10 | 10 | 1 | 1 |
-X | 1 | 1 | 1 | 0 | 1 | 0 | 1 | 1 | 10 | 0 |
-Y | -8 | 1 | -8 | 0 | 1 | -8 | 1 | 1 | 0 | 10 |
-
-This nucleotide matrix was introduced in
- Jalview 2.8. If you'd like to improve it - please take a look at Issue JAL-1027
- - introduce a nucleotide substitution matrix that supports RNA/DNA
- and ambiguity codes
-
-
-
-
-
+
+