--- /dev/null
+ScoreMatrix DNA
+ACGTUIXRYN -
+#
+# A DNA substitution matrix.
+# 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.
+#
+# The first line declares a ScoreMatrix with the name DNA (shown in menus)
+# The second line gives the symbols for which scores are held in the matrix
+# These may include a space (but not as the first or last character)
+# Scores are not case sensitive, unless column(s) are provided for lower case characters
+#
+#
+# Comment line with symbols is provided as a guide
+# Values may be integer or floating point, delimited by tab, space, comma or combinations
+#
+# A C G T U I X R Y N -
+#
+ 10 -8 -8 -8 -8 1 1 1 -8 1 1 1
+ -8 10 -8 -8 -8 1 1 -8 1 1 1 1
+ -8 -8 10 -8 -8 1 1 1 -8 1 1 1
+ -8 -8 -8 10 10 1 1 -8 1 1 1 1
+ -8 -8 -8 10 10 1 1 -8 1 1 1 1
+ 1 1 1 1 1 10 0 0 0 1 1 1
+ 1 1 1 1 1 0 10 0 0 1 1 1
+ 1 -8 1 -8 -8 0 0 10 -8 1 1 1
+ -8 1 -8 1 1 0 0 -8 10 1 1 1
+ 1 1 1 1 1 1 1 1 1 10 1 1
+ 1 1 1 1 1 1 1 1 1 1 1 1
+ 1 1 1 1 1 1 1 1 1 1 1 1
+#
+# A C G T U I X R Y N -