| ! | Bio.Sequence.SeqData, Bio.Sequence |
| ? | Bio.Sequence.SeqData |
| Ala | Bio.Sequence.SeqData, Bio.Sequence |
| Alignment | Bio.Alignment.AlignData |
| Amino | Bio.Sequence.SeqData, Bio.Sequence |
| Ann | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
| Annotation | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
| appendHeader | Bio.Sequence.SeqData, Bio.Sequence |
| Arg | Bio.Sequence.SeqData, Bio.Sequence |
| Asm | Bio.Alignment.ACE |
| Asn | Bio.Sequence.SeqData, Bio.Sequence |
| Asp | Bio.Sequence.SeqData, Bio.Sequence |
| Assembly | Bio.Alignment.ACE |
| Asx | Bio.Sequence.SeqData, Bio.Sequence |
| Aux | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat |
| aux |
| 1 (Function) | Bio.Alignment.BlastData |
| 2 (Function) | Bio.Alignment.BlastFlat |
| bits |
| 1 (Function) | Bio.Alignment.BlastData |
| 2 (Function) | Bio.Alignment.BlastFlat |
| blastdate | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat |
| BlastFlat |
| 1 (Type/Class) | Bio.Alignment.BlastFlat |
| 2 (Data Constructor) | Bio.Alignment.BlastFlat |
| BlastHit |
| 1 (Type/Class) | Bio.Alignment.BlastData |
| 2 (Data Constructor) | Bio.Alignment.BlastData |
| BlastMatch |
| 1 (Type/Class) | Bio.Alignment.BlastData |
| 2 (Data Constructor) | Bio.Alignment.BlastData |
| blastn_default | Bio.Alignment.Matrices |
| blastprogram | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat |
| BlastRecord |
| 1 (Type/Class) | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat |
| 2 (Data Constructor) | Bio.Alignment.BlastData |
| blastreferences | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat |
| BlastResult |
| 1 (Type/Class) | Bio.Alignment.BlastData |
| 2 (Data Constructor) | Bio.Alignment.BlastData |
| blastversion | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat |
| blosum45 | Bio.Alignment.Matrices |
| blosum62 | Bio.Alignment.Matrices |
| blosum80 | Bio.Alignment.Matrices |
| Branch | Bio.Clustering |
| Chr | Bio.Alignment.AlignData |
| Clustered | Bio.Clustering |
| cluster_sl | Bio.Clustering |
| columns | Bio.Alignment.AlignData |
| Comp | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
| compact | Bio.Sequence.HashWord |
| compl | Bio.Sequence.SeqData, Bio.Sequence |
| complement | Bio.Sequence.HashWord |
| contig | Bio.Alignment.ACE |
| contigous | Bio.Sequence.HashWord, Bio.Sequence |
| countIO | Bio.Util |
| countSeqs | Bio.Sequence.Fasta |
| Cys | Bio.Sequence.SeqData, Bio.Sequence |
| database | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat |
| dbchars | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat |
| dbsequences | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat |
| decode2Bit | Bio.Sequence.TwoBit, Bio.Sequence |
| decomment | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
| Del | Bio.Alignment.AlignData |
| Dir | Bio.Alignment.AlignData |
| Edit | Bio.Alignment.AlignData |
| EditList | Bio.Alignment.AlignData |
| entropy | Bio.Sequence.Entropy, Bio.Sequence |
| eval | Bio.Alignment.AlignData |
| EvidenceCode | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
| extractGaps | Bio.Alignment.AlignData |
| e_val |
| 1 (Function) | Bio.Alignment.BlastData |
| 2 (Function) | Bio.Alignment.BlastFlat |
| flatten | Bio.Alignment.BlastFlat |
| fragments | Bio.Alignment.ACE |
| Frame | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat |
| fromIUPAC | Bio.Sequence.SeqData, Bio.Sequence |
| fromStr | Bio.Sequence.SeqData, Bio.Sequence |
| Func | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
| Fwd | Bio.Alignment.AlignData |
| gapped | Bio.Sequence.HashWord |
| Gaps | Bio.Alignment.AlignData |
| genkeys | Bio.Sequence.HashWord |
| Gln | Bio.Sequence.SeqData, Bio.Sequence |
| global_align |
| 1 (Function) | Bio.Alignment.SAlign |
| 2 (Function) | Bio.Alignment.AAlign |
| 3 (Function) | Bio.Alignment.QAlign |
| global_score |
| 1 (Function) | Bio.Alignment.SAlign |
| 2 (Function) | Bio.Alignment.AAlign |
| 3 (Function) | Bio.Alignment.QAlign |
| Glu | Bio.Sequence.SeqData, Bio.Sequence |
| Glx | Bio.Sequence.SeqData, Bio.Sequence |
| Gly | Bio.Sequence.SeqData, Bio.Sequence |
| GO | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
| GoClass | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
| GoDef |
| 1 (Type/Class) | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
| 2 (Data Constructor) | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
| GoHierarchy | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
| GoTerm | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
| hash | Bio.Sequence.HashWord, Bio.Sequence |
| hashes | Bio.Sequence.HashWord, Bio.Sequence |
| HashF | Bio.Sequence.HashWord, Bio.Sequence |
| hasqual | Bio.Sequence.SeqData |
| HF | Bio.Sequence.HashWord, Bio.Sequence |
| His | Bio.Sequence.SeqData, Bio.Sequence |
| hits | Bio.Alignment.BlastData |
| hRead2Bit | Bio.Sequence.TwoBit, Bio.Sequence |
| hReadFasta | Bio.Sequence.Fasta, Bio.Sequence |
| hReadPhd | Bio.Sequence.Phd, Bio.Sequence |
| hWriteFasta | Bio.Sequence.Fasta, Bio.Sequence |
| hWriteFastaQual | Bio.Sequence.Fasta, Bio.Sequence |
| hWriteQual | Bio.Sequence.Fasta, Bio.Sequence |
| h_from |
| 1 (Function) | Bio.Alignment.BlastData |
| 2 (Function) | Bio.Alignment.BlastFlat |
| h_to |
| 1 (Function) | Bio.Alignment.BlastData |
| 2 (Function) | Bio.Alignment.BlastFlat |
| IC | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
| IDA | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
| identity |
| 1 (Function) | Bio.Alignment.BlastData |
| 2 (Function) | Bio.Alignment.BlastFlat |
| IEA | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
| IEP | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
| IGC | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
| IGI | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
| Ile | Bio.Sequence.SeqData, Bio.Sequence |
| IMP | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
| indirect | Bio.Alignment.Multiple |
| Ins | Bio.Alignment.AlignData |
| insertGaps | Bio.Alignment.AlignData |
| IPI | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
| isCurated | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
| isN | Bio.Sequence.HashWord |
| isRepl | Bio.Alignment.AlignData |
| ISS | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
| k2n | Bio.Sequence.HashWord |
| k2n' | Bio.Sequence.HashWord |
| ksort | Bio.Sequence.HashWord, Bio.Sequence |
| KWords | Bio.Sequence.Entropy, Bio.Sequence |
| kwords | Bio.Sequence.Entropy, Bio.Sequence |
| lazyMany | Bio.Util.Parsex |
| Leaf | Bio.Clustering |
| Leu | Bio.Sequence.SeqData, Bio.Sequence |
| lines | Bio.Util |
| local_align |
| 1 (Function) | Bio.Alignment.SAlign |
| 2 (Function) | Bio.Alignment.AAlign |
| 3 (Function) | Bio.Alignment.QAlign |
| local_score |
| 1 (Function) | Bio.Alignment.SAlign |
| 2 (Function) | Bio.Alignment.AAlign |
| 3 (Function) | Bio.Alignment.QAlign |
| Lys | Bio.Sequence.SeqData, Bio.Sequence |
| matches | Bio.Alignment.BlastData |
| Met | Bio.Sequence.SeqData, Bio.Sequence |
| Minus | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat |
| mkSeqs | Bio.Sequence.Fasta |
| mylines | Bio.Util |
| n2i' | Bio.Sequence.HashWord |
| n2k | Bio.Sequence.HashWord |
| NAS | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
| ND | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
| NR | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
| Offset | Bio.Sequence.SeqData, Bio.Sequence |
| on | Bio.Alignment.AlignData |
| overlap_align | Bio.Alignment.QAlign |
| overlap_score | Bio.Alignment.QAlign |
| pam30 | Bio.Alignment.Matrices |
| pam70 | Bio.Alignment.Matrices |
| parse | Bio.Alignment.Blast |
| Phe | Bio.Sequence.SeqData, Bio.Sequence |
| Plus | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat |
| Pro | Bio.Sequence.SeqData, Bio.Sequence |
| Proc | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
| progressive | Bio.Alignment.Multiple |
| ptest | Bio.Alignment.ACE |
| qlength |
| 1 (Function) | Bio.Alignment.BlastData |
| 2 (Function) | Bio.Alignment.BlastFlat |
| Qual | Bio.Sequence.SeqData, Bio.Sequence |
| QualData | Bio.Sequence.SeqData, Bio.Sequence |
| qualMx | Bio.Alignment.QAlign |
| query |
| 1 (Function) | Bio.Alignment.BlastData |
| 2 (Function) | Bio.Alignment.BlastFlat |
| q_from |
| 1 (Function) | Bio.Alignment.BlastData |
| 2 (Function) | Bio.Alignment.BlastFlat |
| q_to |
| 1 (Function) | Bio.Alignment.BlastData |
| 2 (Function) | Bio.Alignment.BlastFlat |
| RCA | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
| rcontig | Bio.Sequence.HashWord, Bio.Sequence |
| rcpacked | Bio.Sequence.HashWord, Bio.Sequence |
| read2Bit | Bio.Sequence.TwoBit, Bio.Sequence |
| readACE | Bio.Alignment.ACE |
| readFasta | Bio.Sequence.Fasta, Bio.Sequence |
| readFastaQual | Bio.Sequence.Fasta, Bio.Sequence |
| readGO | Bio.Sequence.GOA |
| readGOA | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
| readObo | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
| readPhd | Bio.Sequence.Phd, Bio.Sequence |
| readQual | Bio.Sequence.Fasta, Bio.Sequence |
| reads | Bio.Alignment.ACE |
| readTerms | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
| readXML |
| 1 (Function) | Bio.Alignment.BlastXML |
| 2 (Function) | Bio.Alignment.BlastFlat |
| Repl | Bio.Alignment.AlignData |
| results | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat |
| Rev | Bio.Alignment.AlignData |
| revcompl | Bio.Sequence.SeqData, Bio.Sequence |
| Selector | Bio.Alignment.AlignData |
| Seq | Bio.Sequence.SeqData, Bio.Sequence |
| SeqData | Bio.Sequence.SeqData, Bio.Sequence |
| seqdata | Bio.Sequence.SeqData, Bio.Sequence |
| seqheader | Bio.Sequence.SeqData, Bio.Sequence |
| SeqId | Bio.Alignment.BlastData |
| seqlabel | Bio.Sequence.SeqData, Bio.Sequence |
| seqlength | Bio.Sequence.SeqData, Bio.Sequence |
| seqqual | Bio.Sequence.SeqData, Bio.Sequence |
| Sequence | Bio.Sequence.SeqData, Bio.Sequence |
| sequence' | Bio.Util |
| Ser | Bio.Sequence.SeqData, Bio.Sequence |
| setHeader | Bio.Sequence.SeqData, Bio.Sequence |
| Shape | Bio.Sequence.HashWord |
| showalign | Bio.Alignment.AlignData |
| simpleMx | Bio.Alignment.Matrices |
| slength |
| 1 (Function) | Bio.Alignment.BlastData |
| 2 (Function) | Bio.Alignment.BlastFlat |
| splitWhen | Bio.Util |
| STP | Bio.Sequence.SeqData, Bio.Sequence |
| Strand | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat |
| Strands | Bio.Alignment.BlastData, Bio.Alignment.BlastFlat |
| subject |
| 1 (Function) | Bio.Alignment.BlastData |
| 2 (Function) | Bio.Alignment.BlastFlat |
| SubstMx | Bio.Alignment.AlignData |
| TAS | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
| test | Bio.Alignment.QAlign |
| Thr | Bio.Sequence.SeqData, Bio.Sequence |
| toIUPAC | Bio.Sequence.SeqData, Bio.Sequence |
| toStr | Bio.Sequence.SeqData, Bio.Sequence |
| toStrings | Bio.Alignment.AlignData |
| translate | Bio.Sequence.SeqData, Bio.Sequence |
| Trp | Bio.Sequence.SeqData, Bio.Sequence |
| Tyr | Bio.Sequence.SeqData, Bio.Sequence |
| UniProtAcc | Bio.Sequence.GeneOntology, Bio.Sequence.GOA |
| unval | Bio.Sequence.HashWord |
| Val | Bio.Sequence.SeqData, Bio.Sequence |
| val | Bio.Sequence.HashWord |
| writeACE | Bio.Alignment.ACE |
| writeFasta | Bio.Sequence.Fasta, Bio.Sequence |
| writeFastaQual | Bio.Sequence.Fasta, Bio.Sequence |
| writeQual | Bio.Sequence.Fasta, Bio.Sequence |
| Xaa | Bio.Sequence.SeqData, Bio.Sequence |
| Xle | Bio.Sequence.SeqData, Bio.Sequence |
