- Blast
- BlastTool
- BlastN
- Dust
- FilteringDB
- IndexName
- MinRawGappedScore
- NonGreedy
- OffDiagonalRange
- Penalty
- PercentIdentity
- Reward
- SoftMaskingN
- BlastNTask
- BlastNTaskType
- TemplateLength
- TemplateLengthValue
- TemplateType
- TemplateTypeType
- UseIndex
- WindowMaskerDB
- WindowMaskerTaxID
- BlastP
- BlastPTask
- BlastPTaskType
- CompBasedStatsP
- CompBasedStatsPValue
- ScoringMatrixP
- ScoringMatrixPType
- SegP
- SoftMaskingP
- WordSizeP
- BlastX
- BlastXTask
- BlastXTaskType
- CompBasedStatsX
- CompBasedStatsXValue
- ScoringMatrixX
- ScoringMatrixXType
- SegX
- SoftMaskingX
- WordSizeX
- BlastCLI
- BlastQueryBase
- BlastQueryWithIPG
- BlastQueryWithLists
- FlagsKt
- AutoCPUCores
- AutoCPUCoresValue
- BestHitOverhang
- BestHitScoreEdge
- CullingLimit
- DBFile
- DBGenCode
- DBHardMask
- DBSize
- DBSoftMask
- EntrezQuery
- ExpectValue
- GIList
- GapExtend
- GapOpen
- GapTrigger
- HTML
- HelpLong
- HelpShort
- IPGList
- InPSSMFile
- InclusionEValueThreshold
- LineLength
- LowercaseMasking
- MaxHSPs
- MaxIntronLength
- MaxTargetSeqs
- MultiThreadingMode
- MultiThreadingModeValue
- NegativeGIList
- NegativeIPGList
- NegativeSeqIDList
- NegativeTaxIDList
- NegativeTaxIDs
- NumAlignments
- NumCPUCores
- NumDescriptions
- NumIterations
- OutASCIIPSSMFile
- OutFile
- OutFormat
- FormatDelimiter
- FormatFields
- FormatType
- FormatField
- OutPSSMFile
- ParseDefLines
- PseudoCount
- QueryCoverageHSPPercent
- QueryFile
- QueryGenCode
- QueryLocation
- Remote
- SaveEachPSSM
- SavePSSMAfterLastRound
- SearchSpace
- ImportSearchStrategy
- ExportSearchStrategy
- Seg
- SeqIDList
- ShowGIs
- SortHSPs
- HSPSorting
- SortHits
- HitSorting
- Strand
- StrandType
- SubjectBestHit
- SubjectFile
- SubjectLocation
- SumStats
- TaxIDList
- TaxIDs
- Threshold
- UngappedAlignmentsOnly
- UseSmithWatermanTraceback
- Version
- WindowSize
- ExtensionDropoffUngapped
- ExtensionDropoffPrelimGapped
- ExtensionDropoffFinalGapped
- DeltaBlast
- CompBasedStatsDelta
- CompBasedStatsDeltaValue
- DomainInclusionEValueThreshold
- MatrixDelta
- MatrixDeltaType
- RPSDB
- SegDelta
- ShowDomainHits
- SoftMaskingDelta
- WordSizeDelta
- ErrorMap
- BlastFormatter
- Archive
- RID
- PSIBlast
- CompBasedStatsPSI
- CompBasedStatsPSIValue
- IgnoreMSAMaster
- InMSAFile
- MSAMasterIndex
- MatrixPSI
- MatrixPSIType
- PHIPatternFile
- SegPSI
- SoftMaskingPSI
- WordSizePSI
- RPSBlast
- CompBasedStatsRPS
- CompBasedStatsRPSValue
- SegRPS
- SoftMaskingRPS
- RPSTBlastN
- CompBasedStatsRPSTN
- CompBasedStatsRPSTNValue
- SegRPSTN
- SoftMaskingRPSTN
- BlastCommand
- BlastField
- TBlastN
- CompBasedStatsTN
- CompBasedStatsTNValue
- ScoringMatrixTN
- ScoringMatrixTNType
- SegTN
- SoftMaskingTN
- TBlastNTask
- TBlastNTaskValue
- WordSizeTBlastN
- TBlastX
- ScoringMatrixTX
- ScoringMatrixTXType
- SegTX
- SoftMaskingTX
- WordSizeTX