X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Fscorematrices.html;h=5c4a498f781ac8e00391ab57519e7bf90d9bca42;hb=68dcaa7437590985b988a95338a36821c0ee641e;hp=3858b53411fe3e42ae24ffcacacd021c15a8778a;hpb=d5538cea7610ca0658449f0bcdb8a7063c3c90fe;p=jalview.git diff --git a/help/html/calculations/scorematrices.html b/help/html/calculations/scorematrices.html index 3858b53..5c4a498 100644 --- a/help/html/calculations/scorematrices.html +++ b/help/html/calculations/scorematrices.html @@ -1,22 +1,24 @@ + -->
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 |