| Interface | Description |
|---|---|
| ScoreMatrix |
| Class | Description |
|---|---|
| AminoAcidScores | |
| Blosum45 | |
| Blosum50 | |
| Blosum55 | |
| Blosum60 | |
| Blosum62 | |
| Blosum65 | |
| Blosum70 | |
| Blosum75 | |
| Blosum80 | |
| Blosum85 | |
| Blosum90 | |
| Hamming | |
| JukesCantor |
Jukes Cantor assumes equal substitution frequencies and equal nucleotide
equilibrium frequencies.
|
| NucleotideScores | |
| Pam100 | |
| Pam110 | |
| Pam120 | |
| Pam130 | |
| Pam140 | |
| Pam150 | |
| Pam160 | |
| Pam170 | |
| Pam180 | |
| Pam190 | |
| Pam200 | |
| Pam210 | |
| Pam220 | |
| Pam230 | |
| Pam240 | |
| Pam250 | |
| Scores |
Base class for all score matrices in the package.
|
| ScoresFactory | |
| SubstScoreMatrix |
http://code.google.com/p/jebl2/