X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Fcalculations%2Fscorematrices.html;h=5fbbc194f2dde467cf88aad0e748c9d188dd40c7;hb=550949340ef5ccd5757dd50b11b9613d61571046;hp=100e21c669cb3f20717f86cdb4b583e7ab74c39b;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git diff --git a/help/html/calculations/scorematrices.html b/help/html/calculations/scorematrices.html index 100e21c..5fbbc19 100644 --- a/help/html/calculations/scorematrices.html +++ b/help/html/calculations/scorematrices.html @@ -1,113 +1,1664 @@ + -->
Jalview includes a small number of built in substitution matrices, used for different types of analysis.
-Jalview includes a small number of built in substitution + matrices, used for different types of analysis.
++ | 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 | +
+ 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 | +