Substitution Matrices available in Jalview
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.
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
| 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