X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Fscorematrices.html;h=cb07a498ad4a1451542ddc06a1060d9238019587;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=eb8b194586c96784dccfd78311ce4327d0dd37be;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git
diff --git a/help/html/calculations/scorematrices.html b/help/html/calculations/scorematrices.html
index eb8b194..cb07a49 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
Substitution matrices in Jalview
@@ -24,9 +27,10 @@
Jalview includes a small number of built in substitution matrices, used for different types of analysis.
- BLOSUM62 is the standard protein sequence alignment and analysis matrix.
-- PAM250 is another standard protein matrix, but not currently available for use from Jalview's user interface.
-- Simple Nucleotide Substition is a (fairly) arbitrary DNA/RNA substitution matrix.
-
+- PAM250 is another standard protein matrix, and (since 2.8.1) is available for Tree and PCA calculations.
+- Simple Nucleotide Substition is a (fairly) arbitrary DNA/RNA substitution matrix.
+
BLOSUM62
@@ -58,6 +62,8 @@
| 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 |
@@ -86,7 +92,7 @@
| 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.
@@ -108,5 +114,100 @@ In addition, it encodes weak equivalence between R and Y with AG and CTU, respec
- introduce a nucleotide substitution matrix that supports RNA/DNA
and ambiguity codes
+
+
+