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, and (since 2.8.1) is available for Tree and PCA calculations.
• Simple Nucleotide Substitution is a (fairly) arbitrary DNA/RNA substitution matrix.

BLOSUM62

	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

This nucleotide matrix was introduced in Jalview 2.8. If you'd like to improve it - please take a look at Issue JAL-1027 - introduce a nucleotide substitution matrix that supports RNA/DNA and ambiguity codes