MPGAfold Configuration Parameters
Configuration Parameters
- TotalPhysicalPES
- TotalVirtualPES
- MultipleRunSuffixes
- StartRun
- StopRun
- NumGen
- NumFill
- OutputStart
- OutputIncr
- NBest
- RNGSeed
- PopPressure
- SequenceFile
- SeqRange
- FilePrefix
- OutputPath
- UseSubDirs
Window Parameters
- WindowWidth
- ConvergenceCriteria
Energy Parameters
- EnergyRule
- EnergyTableFile
- PKEnergyTableFile
- StartUseDanglingGen
- StartUseDanglingScore
- BoltzmannFlag
- GAILRuleFlag
- Efn2energyTableFile
- Efn2Flag
Stem Parameters
- MinStemLength
- StemTableFile
- AddStemFile
- StemTableFlag
- MotifFlag
- PrintMotifTableFlag
- Loop1by1
- Loop1by2and2by1
- Loop2by2
- LoopBulge
- BulgeMotifSize
- MotifTableFile
- ForbidStemFile
- EmbedStemFile
- EmbedGens
- EmbedProb
- ForceStemFile
- StickyStemFile
- DoCentralStickyStems
- DoParentStickyStems
Peelback Parameters
- PeelToFitProb
- DoMutPeelToFit
- DoCrossPeelToFit
- DoNumfillPeelToFit
- UnzipProb
- PeelBack
- GUClose
- PeelGUOnly
Sequential Folding Parameters
- SequentialFoldFlag
- GensPerNuc
- StartSeqMax
- NTsPerExtend
- SeqMin
Pseudoknot Parameters
- PKFlag
- PKCaptureFlag
- PKNumCritGens
Display Parameters
- DisplayHost
- DisplaySockNum
- DisplayFlag
- PKDisplayFlag
- TargetEnergy
- ClampFitDisp
- SyncFlag
Intermediate Solution Output Parameters
- DumpSolFlag
- DumpSolType
- PhyPIDNumForSol
- VirPIDNumForSol
- PIDFlag
- PlotFlag
- ThreeDFlag
- DumpEfn2SolFlag
Trace Parameters
- TraceFile
- DumpTraceHits
- TraceStemUnion
Other Parameters
- SelectionMethod
- CrossoverMethod
- EvalFlag
- Optimization