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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
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