| score | Bio.Chain.Alignment.Type, Bio.Chain.Alignment |
| scoreMatrix | Bio.Chain.Alignment.Type |
| Scoring | Bio.Chain.Alignment.Type |
| scoring | Bio.Chain.Alignment.Scoring.Loader, Bio.Chain.Alignment.Scoring |
| ScoringMatrix | Bio.Chain.Alignment.Scoring.Loader, Bio.Chain.Alignment.Scoring |
| SD | Bio.Utils.IUPAC |
| sd | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| semi | Bio.Chain.Alignment.Type |
| SemiglobalAlignment | |
| 1 (Type/Class) | Bio.Chain.Alignment.Algorithms, Bio.Chain.Alignment |
| 2 (Data Constructor) | Bio.Chain.Alignment.Algorithms, Bio.Chain.Alignment |
| semiStart | Bio.Chain.Alignment.Algorithms |
| sequence1 | Bio.Chain.Alignment.Type, Bio.Chain.Alignment |
| sequence2 | Bio.Chain.Alignment.Type, Bio.Chain.Alignment |
| SequenceAlignment | Bio.Chain.Alignment.Type |
| SER | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| Serine | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| set | Bio.Molecule |
| SG | Bio.Utils.IUPAC |
| sg | Bio.Protein.AminoAcid.Type, Bio.Protein.AminoAcid |
| similarity | Bio.Chain.Alignment |
| similarity' | Bio.Chain.Alignment |
| similarityGen | Bio.Chain.Alignment |
| similarityGen' | Bio.Chain.Alignment |
| SimpleGap | Bio.Chain.Alignment.Type, Bio.Chain.Alignment |
| SimpleGap2 | Bio.Chain.Alignment.Type, Bio.Chain.Alignment |
| singleton | Bio.Molecule |
| Stop | Bio.Chain.Alignment.Type |
| substitute | Bio.Chain.Alignment.Algorithms |
| substituteED | Bio.Chain.Alignment.Algorithms |
| Substitution | Bio.Chain.Alignment.Scoring.TH |
| svd3 | Bio.Utils.Geometry |
| Symbol | Bio.Utils.Monomer, Bio.Protein.AminoAcid, Bio.NucleicAcid.Nucleotide |
| symbol | Bio.Utils.Monomer, Bio.Protein.AminoAcid, Bio.NucleicAcid.Nucleotide |