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| Interface Summary | |
|---|---|
| ScoreMatrix | |
| Class Summary | |
|---|---|
| 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 | |
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