X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=help%2Fhtml%2Fcalculations%2Fscorematrices.html;h=5c4a498f781ac8e00391ab57519e7bf90d9bca42;hb=68dcaa7437590985b988a95338a36821c0ee641e;hp=eb8b194586c96784dccfd78311ce4327d0dd37be;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git
diff --git a/help/html/calculations/scorematrices.html b/help/html/calculations/scorematrices.html
index eb8b194..5c4a498 100644
--- a/help/html/calculations/scorematrices.html
+++ b/help/html/calculations/scorematrices.html
@@ -1,21 +1,24 @@
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see
Jalview includes a small number of built in substitution matrices, used for different types of analysis.
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 |
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 +
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.