1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
|
#
# VTML200
#
# This matrix was produced by scripts written by
# Kai Kneutgen and Tobias Mueller [Mai-2002]
#
# VTML200 substitution matrix, Units = Third-Bits
#
# Expected Score = -1.038 Third-Bits
# Lowest Score = -6.432
# Highest Score = 15.127
# Entropy H = 0.420 Bits
#
#
# For further information on the VTML substitution model, see
#
# Estimating Amino Acid Substitution Models:
# A Comparison of Dayhoff's Estimator, the Resolvent Approach and a Maximum Likelihood Method.
# T. Mueller, R. Spang and M. Vingron
# Mol Biol Evol 19(1): 8-13. 2002.
#
# or mail to
# Tobias.Mueller@molgen.mpg.de
#
# The latest version of this perl script can be downloaded at
# https://www.molgen.mpg.de/~muelle_t
#
# added J-Column as (I+L)/2 and U == X
# reordered to be (alphabetically sorted; X *)
A B C D E F G H I J K L M N O P Q R S T U V W Y Z X *
A 4 -1 1 -1 -1 -3 0 -2 -1 -2 -1 -2 -1 -1 -1 0 -1 -2 1 1 -1 0 -4 -3 -1 -1 -6
B -1 4 -3 5 2 -5 0 1 -4 -5 0 -5 -3 4 -1 -1 1 -1 1 0 -1 -3 -5 -3 1 -1 -6
C 1 -3 12 -4 -4 -3 -2 -2 0 -2 -4 -3 -1 -2 -1 -3 -3 -3 1 0 -1 1 -6 0 -4 -1 -6
D -1 5 -4 6 3 -6 -1 0 -5 -5 0 -5 -4 3 -2 -1 1 -2 0 -1 -2 -4 -6 -4 2 -2 -6
E -1 2 -4 3 5 -5 -1 0 -4 -4 1 -4 -3 1 -1 -1 2 -1 0 -1 -1 -3 -6 -3 4 -1 -6
F -3 -5 -3 -6 -5 8 -5 0 0 1 -5 2 1 -4 -1 -4 -3 -4 -3 -3 -1 -1 3 5 -4 -1 -6
G 0 0 -2 -1 -1 -5 8 -2 -6 -6 -2 -5 -4 0 -2 -2 -2 -2 0 -2 -2 -4 -5 -5 -2 -2 -6
H -2 1 -2 0 0 0 -2 8 -3 -3 0 -2 -3 1 0 -2 2 1 0 -1 0 -3 -1 3 1 0 -6
I -1 -4 0 -5 -4 0 -6 -3 5 4 -3 3 2 -4 -1 -4 -3 -3 -3 -1 -1 4 -2 -2 -3 -1 -6
J -2 -5 -2 -5 -4 1 -6 -3 4 4 -3 4 3 -4 -1 -4 -3 -3 -3 -2 -1 3 -2 -2 -3 -1 -6
K -1 0 -4 0 1 -5 -2 0 -3 -3 5 -3 -2 1 -1 -1 2 4 0 0 -1 -3 -4 -3 2 -1 -6
L -2 -5 -3 -5 -4 2 -5 -2 3 4 -3 5 3 -4 -1 -3 -2 -3 -3 -2 -1 2 -1 -1 -3 -1 -6
M -1 -3 -1 -4 -3 1 -4 -3 2 3 -2 3 6 -3 -1 -3 -1 -2 -2 -1 -1 2 -3 -2 -2 -1 -6
N -1 4 -2 3 1 -4 0 1 -4 -4 1 -4 -3 6 -1 -2 1 0 1 0 -1 -3 -5 -2 1 -1 -6
O -1 -1 -1 -2 -1 -1 -2 0 -1 -1 -1 -1 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -2 -1 -1 -1 -6
P 0 -1 -3 -1 -1 -4 -2 -2 -4 -4 -1 -3 -3 -2 -2 9 -1 -1 0 -1 -2 -3 -4 -5 -1 -2 -6
Q -1 1 -3 1 2 -3 -2 2 -3 -3 2 -2 -1 1 -1 -1 5 2 0 0 -1 -2 -6 -3 4 -1 -6
R -2 -1 -3 -2 -1 -4 -2 1 -3 -3 4 -3 -2 0 -1 -1 2 7 -1 -1 -1 -3 -3 -2 0 -1 -6
S 1 1 1 0 0 -3 0 0 -3 -3 0 -3 -2 1 -1 0 0 -1 4 2 -1 -2 -4 -2 0 -1 -6
T 1 0 0 -1 -1 -3 -2 -1 -1 -2 0 -2 -1 0 -1 -1 0 -1 2 4 -1 0 -5 -3 -1 -1 -6
U -1 -1 -1 -2 -1 -1 -2 0 -1 -1 -1 -1 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -2 -1 -1 -1 -6
V 0 -3 1 -4 -3 -1 -4 -3 4 3 -3 2 2 -3 -1 -3 -2 -3 -2 0 -1 4 -4 -2 -3 -1 -6
W -4 -5 -6 -6 -6 3 -5 -1 -2 -2 -4 -1 -3 -5 -2 -4 -6 -3 -4 -5 -2 -4 15 4 -6 -2 -6
Y -3 -3 0 -4 -3 5 -5 3 -2 -2 -3 -1 -2 -2 -1 -5 -3 -2 -2 -3 -1 -2 4 9 -3 -1 -6
Z -1 1 -4 2 4 -4 -2 1 -3 -3 2 -3 -2 1 -1 -1 4 0 0 -1 -1 -3 -6 -3 4 -1 -6
X -1 -1 -1 -2 -1 -1 -2 0 -1 -1 -1 -1 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -2 -1 -1 -1 -6
* -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 1
|
