#################################################################
###################### GENERAL PARAMETERS #######################
#################################################################
EuGene.version		4.1
EuGene.organism	artemia franciscana
EuGene.mode		Eukaryote  # Eukaryote or Prokaryote
EuGene.sloppy		0
EuGene.VerboseGC	0
EuGene.GCLatency	100000
#
##### Lengths #####
EuGene.InitExDist	/scratch/protist/ARTEMIA/data/models/init.dist
EuGene.IntrExDist	/scratch/protist/ARTEMIA/data/models/intr.dist
EuGene.TermExDist	/scratch/protist/ARTEMIA/data/models/term.dist
EuGene.SnglExDist	/scratch/protist/ARTEMIA/data/models/sngl.dist
EuGene.IntronDist	/scratch/protist/ARTEMIA/data/models/intron.dist
EuGene.InterGDist	/scratch/protist/ARTEMIA/data/models/intergenic.dist
EuGene.5PrimeDist	/scratch/protist/ARTEMIA/data/models/utr.dist
EuGene.3PrimeDist	/scratch/protist/ARTEMIA/data/models/utr.dist
EuGene.RnaDist		/scratch/protist/ARTEMIA/data/models/rna.dist
EuGene.OverlapDist	/scratch/protist/ARTEMIA/data/models/overlap.dist
EuGene.UIRDist		/scratch/protist/ARTEMIA/data/models/uir_prok.dist # only used in Prokaryote mode
#
##### Priors #####
EuGene.SplicedStopPen   1e999.0
EuGene.ExonPrior	0.33		# Prior on the initial states
EuGene.IntronPrior	0.17		# Sato et al 1999 / Terryn et al. 1999
EuGene.InterPrior	0.4
EuGene.FivePrimePrior	0.03
EuGene.ThreePrimePrior	0.07
EuGene.RnaPrior         0.03
EuGene.RnaPrior         0.03
EuGene.BiCodingPrior    0.00
EuGene.UIRPrior         0.00
#
##### Codon table #####
EuGene.CodonTable	euk.codontable # pro.codontable or euk.codontable
#EuGene.NonCanDon     GC
#EuGene.NonCanAcc     AC
#
##
##### Gff3
Gff3.SoTerms		cfg/sofa.obo
##### Output control ######
Output.RemoveFrags	0
Output.UTRtrim		0
Output.MinCDSLen	150
Output.truncate	15
Output.initid		0
Output.stepid		1
Output.graph		0		# Don't produce a graphical output
Output.resx		900
Output.resy		400
Output.glen		-1
Output.golap		-1
Output.gfrom		-1
Output.gto		-1
Output.window		48
Output.offset		0
Output.normopt		1
Output.intron		0
Output.format		l
Output.Prefix		./
Output.webdir		LOCAL # or URL: http://www.inra.fr/bia/T/EuGene/
#
##### Alternative splicing predictor control
AltEst.use			0
AltEst.ExonBorderMatchThreshold 0
AltEst.Penalty			1000
AltEst.includedEstFilter		1
AltEst.compatibleEstFilter	1
AltEst.unsplicedEstFilter		1
AltEst.extremeLengthFilter	1
AltEst.maxEstLength		10000
AltEst.minEstLength		100
AltEst.maxIn				10000
AltEst.minIn				40
AltEst.maxEx				10000
AltEst.minEx				3
AltEst.exonucleasicLength	10
AltEst.RepredictMargin		16000
AltEst.altEstDisplay		0
AltEst.verbose			0
#AltEst.format  		GFF3
#
##### Evaluation mode ######
#Eval.offset   50
Eval.ignoreNpcRNA 1      # Put 1 to ignore the npcRNA for the fitness computing.
Fitness.wsng  1
Fitness.wsne  1
Fitness.wsnn  0
Fitness.wspg  1
Fitness.wspe  1
Fitness.wspn  0
#
##### Operon parameter ######
Operon.maxDistance 10
Operon.initid      0
#
#######################################################################
################### SIGNAL SENSORS PARAMETERS####################
#################################################################
#
##### EuStop parameters #####
EuStop.stopP*	5.526907
#
##### FrameShift parameters #####
FrameShift.Ins*		1e999.0
FrameShift.Del*		1e999.0
#
##### RibosomalFrameShift sensor (uniform penalties) #####
RibosomalFrameShift.type[0]	deletion3   # Possible types: deletion1 deletion2 deletion3 insertion1 insertion2 insertion3
RibosomalFrameShift.pat[0]		AAAAAAC	
RibosomalFrameShift.newStatePos[0] 4	# Position of the new state in the pattern
RibosomalFrameShift.patP*[0]	-10
RibosomalFrameShift.patPNo*[0]	0
RibosomalFrameShift.requiredEstSupport[0]	1 # 1 if an EST support is required
#
##### GeneSplicer parameters #####
GSplicer.coefAcc*	1
GSplicer.penAcc*	0
GSplicer.coefDon*	1
GSplicer.penDon* 	0
#GSplicer.format      GFF3
#
##### PepSignal #####
PepSignal.startP*	1
PepSignal.startB*	0
#PepSignal.format     GFF3
#
##### SpliceMachine parameters #####
SMachine.cmd		"splicemachine.pl "
SMachine.isScaled	0
SMachine.accP*	1.768521
SMachine.accB*	3.233744
SMachine.donP*	2.065017
SMachine.donB*	3.380102
SMachine.startP*	0.052
SMachine.startB*	0.308
SMachine.tSpliceB*	0.0
#SMachine.format      GFF3
#
# NetGene2 parameters #####
NG2.accP*[0]	0.903
NG2.accB*[0]	5.585
NG2.donP*[0]	0.980
NG2.donB*[0]	27.670
NG2.accP*[1]	0.903
NG2.accB*[1]	5.585
NG2.donP*[1]	0.980
NG2.donB*[1]	27.670
#NG2.format           GFF3
#
##### NetStart parameters #####
NStart.startP*		0.052
NStart.startB*		0.308
#
##### ProStart parameters #####
#
ProStart.matchlen	14
ProStart.matchoffset	3
ProStart.RBSPattern attcctcca # E coli (16S genetics/ Steitz J.A.)
ProStart.alpha*	0.4
ProStart.beta*	6.0
ProStart.stackFile stack.dat
ProStart.loopFile loop.dat
#
##### PatConst sensor (uniform penalties) #####
PatConst.type[0]	start
PatConst.pat[0]		ATG
PatConst.newStatePos[0] 1
PatConst.patP*[0]	6.588638
PatConst.patPNo*[0]	-1.395968
#
PatConst.type[1]	donor   # Possible types : start insertion deletion
PatConst.pat[1]		GC	#  transstart transstop stop acceptor donor
PatConst.newStatePos[1] 1       # Position of the new state in the pattern
PatConst.patP*[1]	-4.157315
PatConst.patPNo*[1]	0.225481
#
PatConst.type[2]	donor   # Possible types : start insertion deletion
PatConst.pat[2]		AT	#  transstart transstop stop acceptor donor
PatConst.newStatePos[2] 1       # Position of the new state in the pattern
PatConst.patP*[2]	-4.157315
PatConst.patPNo*[2]	0.225481
#
PatConst.type[3]   acceptor
PatConst.pat[3]	    AC
PatConst.newStatePos[3] 3
PatConst.patP*[3]  -4.157315
PatConst.patPNo*[3]  0.225481
#
##### Sensor SpliceWAM #####
SpliceWAM.MarkovianOrder	1
SpliceWAM.donmodelfilename	WAM/WAM.ARA.DON.L9
SpliceWAM.NbNtBeforeGT		3
SpliceWAM.NbNtAfterGT		4
SpliceWAM.DonScaleCoef*		2.9004
SpliceWAM.DonScalePenalty*	-7.5877
SpliceWAM.accmodelfilename	WAM/WAM.ARA.ACC.L7
SpliceWAM.NbNtBeforeAG		2
SpliceWAM.NbNtAfterAG		3
SpliceWAM.AccScaleCoef*		2.9004
SpliceWAM.AccScalePenalty*	-7.5877
#
##### SplicePredictor parameters #####
SPred.accP*[0]	0.987
SPred.accB*[0]	3.850
SPred.donP*[0]	0.929
SPred.donB*[0]	10.800
SPred.accP*[1]	0.987
SPred.accB*[1]	3.850
SPred.donP*[1]	0.929
SPred.donB*[1]	10.800
#SPred.format GFF3
#
##### Sensor StartWAM #####
StartWAM.modelfilename	WAM/WAM.ARA.START9
StartWAM.NbNtBeforeATG	3
StartWAM.NbNtAfterATG	3
StartWAM.MarkovianOrder	1
StartWAM.ScaleCoef*	0.1594
StartWAM.ScalePenalty*	-3.1439
#
##### Transcript parameters #####
Transcript.Start*	5.599841
Transcript.Stop*	3.473800
Transcript.StartNpc* 30
Transcript.StopNpc* 30
#
#################################################################
################# CONTENT SENSORS PARAMETERS ####################
#################################################################
#
##### Proteic similarity sensor parameters #####
BlastX.PostProcess 0    # 0 1 OR 2
BlastX.PPNumber	   5    # For PostProcess = "2"
BlastX.levels	  0123
BlastX.activegaps NONE
BlastX.level0*	1.800000
BlastX.level1*	1.604000
BlastX.level2*	1.50
BlastX.level3*	0.50
BlastX.level4*	5.0
BlastX.level5*	0.0
BlastX.level6*	0.0
BlastX.level7*	0.0
BlastX.level8*	0.0
BlastX.level9*	0.0
BlastX.blastxM*	5.465044
BlastX.minIn 50
#BlastX.format   GFF3
#
##### Est sensor parameters #####
##################
# NCBI EST >300nt  ## not much mapping
##################
Est.PostProcess[0] 0	# 0 1 OR 2
Est.PPNumber[0]    5	# For PostProcess = "2"
Est.estP*[0]  -8946.971523
#Est.estP*[0]  -1e4  # forces EuGene to match with est
Est.estM[0]   0
Est.utrP*[0]  0.000000
Est.utrM[0]   0
Est.CdsBoost*[0] 1.0
Est.SpliceNonCanP[0] 1.0
Est.SpliceBoost*[0]     0.166893
Est.StrongDonor[0] 0.95
Est.MinDangling[0] 5
Est.MaxIntron[0]   60000
Est.MaxInternalIntron[0]   60000
Est.FileExtension[0]    .est0
Est.mRNAOnly[0] 1
#Est.format[0]    GFF3
#
##################
# RNAseq contigs > 500nt
##################
Est.PostProcess[1] 0	# 0 1 OR 2
Est.PPNumber[1]    5	# For PostProcess = "2"
Est.estP*[1]  -1e4  # forces EuGene to match with est
Est.estM[1]   6
Est.utrP*[1]  0.35
Est.utrM[1]   5
Est.CdsBoost*[1] 0.0
Est.SpliceNonCanP[1] 1.0
Est.SpliceBoost*[1] 1.0
Est.StrongDonor[1] 0.95
Est.MinDangling[1] 3
Est.MaxIntron[1]   60000
Est.MaxInternalIntron[1]   60000
Est.FileExtension[1]    .est1
Est.mRNAOnly[1] 1 
#Est.format[1]    GFF3
#
##################
# RNAseq contigs > 1000nt
##################
Est.PostProcess[2] 0	# 0 1 OR 2
Est.PPNumber[2]    5	# For PostProcess = "2"
Est.estP*[2]  -1e6
Est.estM[2]   6
Est.utrP*[2]  0.35
Est.utrM[2]   5
Est.CdsBoost*[2] 0.0
Est.SpliceNonCanP[2] 1.0
Est.SpliceBoost*[2] 1.0
Est.StrongDonor[2] 0.95
Est.MinDangling[2] 3
Est.MaxIntron[2]   60000
Est.MaxInternalIntron[2]   60000
Est.FileExtension[2]    .est2
Est.mRNAOnly[2] 1 
#Est.format[2]    GFF3
#
##################
# RNAseq junctions
##################
Est.PostProcess[3] 0	# 0 1 OR 2
Est.PPNumber[3]    5	# For PostProcess = "2"
Est.estP*[3]  -1e8
#Est.estP*[3]  -0.4
Est.estM[3]   6
Est.utrP*[3]  0.35
Est.utrM[3]   5
Est.CdsBoost*[3] 10.0
Est.SpliceNonCanP[3] 1.0
Est.SpliceBoost*[3] 10.0
Est.StrongDonor[3] 1011.0
Est.MinDangling[3] 3
Est.MaxIntron[3]   60000
Est.MaxInternalIntron[3]   60000
Est.FileExtension[3]    .est4
Est.mRNAOnly[3] 1 
#Est.format[3]    GFF3
#
##### Homology Sensor parameters #####
Homology.TblastxP*[0]	0
Homology.TblastxB*[0] 	0.0595
Homology.protmatname[0]    BLOSUM80
Homology.MaxHitLen[0]  15000
#Homology.format[0]              GFF3
Homology.FileExtension[0]	.tblastx
Homology.TblastxP*[1]	0
Homology.TblastxB*[1] 	0.0595
Homology.protmatname[1]    BLOSUM80
Homology.MaxHitLen[1]  15000
#Homology.format[1]        GFF3
Homology.FileExtension[1]	.tblastx2
#
##### State penalties per position #####
MarkovConst.minGC[0]	0
MarkovConst.maxGC[0]	100
MarkovConst.Coding*	1.0
MarkovConst.Intron*	1.01
MarkovConst.IntronUTR*	0.98
MarkovConst.UTR5*	0.99
MarkovConst.UTR3*	0.99
MarkovConst.UIR*	0.9
MarkovConst.RNA*	1.0
MarkovConst.Inter*	1.0
#### Pour le brin plus :		# to promote/force prediction on one strand, penalize the other!!
#MarkovConst.minGC[0]    0
#MarkovConst.maxGC[0]    100
#MarkovConst.Coding*    0.00000000000000000000000000000000000000001
#MarkovConst.Intron*    0.00000000000000000000000000000000000000001
#MarkovConst.IntronUTR*    0.00000000000000000000000000000000000000001
#MarkovConst.UTR5*    0.00000000000000000000000000000000000000001
#MarkovConst.UTR3*    0.00000000000000000000000000000000000000001
#MarkovConst.UIR*    0.00000000000000000000000000000000000000001
#MarkovConst.RNA*    0.00000000000000000000000000000000000000001
#MarkovConst.Inter*    1.00
MarkovConst.affectedStrand  0       # 0 (both strands not penalized) or -1 (strand minus) or 1 (strand +plus)
Sensor.MarkovConst.use                   1 
#
##### Interpolated Markov Models parameters #####
MarkovIMM.matname[0]	/ngsprojects/protist/data_archive/ARTEMIA/artemia_IMM.bin
MarkovIMM.minGC[0]	0
MarkovIMM.maxGC[0]	100
MarkovIMM.IntergenicModel[0]	2
MarkovIMM.maxOrder[0]	8
MarkovIMM.npcRNAModel[0] gc
#MarkovIMM.matname[1]	Ara2UTR.mat
#MarkovIMM.minGC[1]	50
#MarkovIMM.maxGC[1]	100
#MarkovIMM.IntergenicModel[1]	2
#MarkovIMM.maxOrder[1]	8
#
##### Markov proteic model parameters #####
MarkovProt.matname[0]	SwP41.noFragm.mininfo1.order2.bin
MarkovProt.minGC[0]	0
MarkovProt.maxGC[0]	100
MarkovProt.maxorder     2
MarkovProt.order        2
#
##### Repeat sensor parameters #####
Repeat.UTRPenalty*	1.0
Repeat.IntronPenalty*	0.001
Repeat.ExonPenalty*	1000000.2
#Repeat.format        GFF3
##### NStretch sensor parameters #####
NStretch.stretchPenalty 1.0
NStretch.maxLengthWithoutPenalty      5000
#
#
##### NcRNA sensor parameters ####
NcRNA.FileExtension[0]  ncrna
NcRNA.NpcRna*[0] 1 
NcRNA.TStartNpc*[0] 1
NcRNA.TStopNpc*[0] 1	
NcRNA.format[0]        GFF3 # Mandatory
#
NcRNA.FileExtension[1]  trna
NcRNA.NpcRna*[1] 1 
NcRNA.TStartNpc*[1] 1
NcRNA.TStopNpc*[1] 1	
NcRNA.format[1]        GFF3 # Mandatory
#
#################################################################
############## SIGNAL/CONTENT SENSORS PARAMETERS ################
#################################################################
#
##### Sensors AnnotaStruct #####
##### augustus #####
AnnotaStruct.FileExtension[0]       augustus # geneid genemark glimmer augustus
AnnotaStruct.TranscriptFeature[0]  gene
AnnotaStruct.Start*[0]             -9.024332
AnnotaStruct.StartType[0]          s     # p: probability  s: score
AnnotaStruct.Stop*[0]              -7.340008
AnnotaStruct.StopType[0]           s
AnnotaStruct.Acc*[0]               3.713457
AnnotaStruct.AccType[0]            s
AnnotaStruct.Don*[0]               3.059103
AnnotaStruct.DonType[0]            s
AnnotaStruct.TrStart*[0]           0
AnnotaStruct.TrStartType[0]        s
AnnotaStruct.TrStop*[0]            0
AnnotaStruct.TrStopType[0]         s
AnnotaStruct.TrStartNpc*[0]        0.5
AnnotaStruct.TrStartNpcType[0]     p
AnnotaStruct.TrStopNpc*[0]         0.5
AnnotaStruct.TrStopNpcType[0]      p
AnnotaStruct.Exon*[0]              1
AnnotaStruct.Intron*[0]            0
AnnotaStruct.CDS*[0]               189760
AnnotaStruct.npcRNA*[0]            0
AnnotaStruct.Intergenic*[0]        0
AnnotaStruct.format[0]             GFF3
#
##### premium protein aln ######
AnnotaStruct.FileExtension[1]     	pep.ASt
AnnotaStruct.TranscriptFeature[1]  gene
AnnotaStruct.Start*[1]             0
AnnotaStruct.StartType[1]          s     # p: probability  s: score
AnnotaStruct.Stop*[1]              0
AnnotaStruct.StopType[1]           s
AnnotaStruct.Acc*[1]               0
AnnotaStruct.AccType[1]            s
AnnotaStruct.Don*[1]               0
AnnotaStruct.DonType[1]            s
AnnotaStruct.TrStart*[1]           0
AnnotaStruct.TrStartType[1]        s
AnnotaStruct.TrStop*[1]            0
AnnotaStruct.TrStopType[1]         s
AnnotaStruct.TrStartNpc*[1]        0
AnnotaStruct.TrStartNpcType[1]     p
AnnotaStruct.TrStopNpc*[1]         0
AnnotaStruct.TrStopNpcType[1]      p
AnnotaStruct.Exon*[1]              0
AnnotaStruct.Intron*[1]            0
AnnotaStruct.CDS*[1]               100
AnnotaStruct.npcRNA*[1]            0
AnnotaStruct.Intergenic*[1]        0
#AnnotaStruct.format[1]             GFF3
#
#
##### IfElse #####
IfElse.SensorIf		NG2
IfElse.SensorElse	SPred
#
##### Riken sensor parameters #####
Riken.StrandRespect			0
Riken.Min_est_diff			100
Riken.Max_overlap			60
Riken.Max_riken_length			60000
Riken.Max_riken_est_length		3000
Riken.Min_riken_length			120 
Riken.Min_riken_est_length		10
Riken.RAFLPenalty*			-120.0
#Riken.format                  		GFF3
#
#################################################################
################## OTHERS SENSORS PARAMETERS ####################
#################################################################
#
##### Sensor GCPlot #####
GCPlot.Color	5
GCPlot.Zoom	2.0
GCPlot.Zoom3	1.0
GCPlot.Up	GC
GCPlot.Over	ATGC
GCPlot.Smooth	100
#
##### GFF sensor parameters #####
GFF.PostProcess		1
#
##### Sensor Plotter
Plotter.GC	 1   # 0 -> no plot  -  1 -> plot 
Plotter.GC3	 1   #
Plotter.A|T/A+T	 0   # T/A+T -> IntronF - A/A+T -> IntronR
#
##### Sensor Tester #####
Tester.Make		SPSN	# SPSN, TEST
Tester.Sensor		EuStop
Tester.Sensor.Instance	0
Tester.SPSN.MinNumbers	100     # greater than 0
Tester.SPSN.Eval        STOP    # START, STOP, SPLICE
#
#################################################################
################# SENSORS CONFIGURATION PARAMETERS ##############
#################################################################
#
##### Sensors activation #####
# SIGNAL SENSORS
Sensor.EuStop.use	1
Sensor.FrameShift.use	0
Sensor.GSplicer.use	0
Sensor.SMachine.use	1
Sensor.NG2.use		0
Sensor.NStart.use	0
Sensor.PatConst.use	2
Sensor.PepSignal.use	0
Sensor.SpliceWAM.use 	0
Sensor.SPred.use	0
Sensor.StartWAM.use	0
Sensor.Transcript.use	1
Sensor.RibosomalFrameShift.use     0
Sensor.ProStart.use	0
#
# CONTENT SENSORS
Sensor.BlastX.use	1
Sensor.Est.use		4
Sensor.Homology.use	0
Sensor.MarkovConst.use	1
Sensor.MarkovIMM.use	1
Sensor.MarkovProt.use	1
Sensor.Repeat.use	1
Sensor.NStretch.use 0
Sensor.NcRNA.use        0
#
# SIGNAL/CONTENT SENSORS
Sensor.AnnotaStruct.use 2
Sensor.IfElse.use	0
Sensor.Riken.use	0
Sensor.QualData.use     0
#
# OTHERS SENSORS
Sensor.GCPlot.use	0
Sensor.GFF.use		0
Sensor.Plotter.use	0
Sensor.Tester.use	0
#
Qual.factor*		5.0
#
##### Sensor priorities	 #####
#  the lower the priority, the first loaded sensor
# SIGNAL SENSORS
Sensor.EuStop 		10
Sensor.FrameShift 	10
Sensor.GSplicer 	10
Sensor.NG2 		10
Sensor.NStart 		10
Sensor.PatConst 	9
Sensor.PepSignal 	10
Sensor.SMachine 	10
Sensor.SpliceWAM 	10
Sensor.SPred 		10
Sensor.StartWAM 	10
Sensor.Transcript 	10
#
# CONTENT SENSORS
Sensor.BlastX 		10
Sensor.Est 		20
Sensor.Homology   	10
Sensor.MarkovConst 	10
Sensor.MarkovIMM 	1
Sensor.MarkovProt 	1
Sensor.Repeat 		9
Sensor.NStretch   1
#
# SIGNAL/CONTENT SENSORS
Sensor.AnnotaStruct     11
Sensor.IfElse 		10
Sensor.Riken 		10
#
# OTHERS SENSORS
Sensor.GCPlot 		1
Sensor.GFF 		10
Sensor.Plotter 		1
Sensor.Tester 		1
#
#
#################################################################
################### OPTIMIZATION PARAMETERS #####################
#################################################################
ParaOptimization.Use 0
ParaOptimization.Regularizer	0.0
#ParaOptimization.TrueCoordFile /scratch/artemia/TRAINING/artfr_true_genes.txt
ParaOptimization.TrueCoordFile /ngsprojects/protist/data_archive/ARTEMIA/trainingSet.aug.sub.txt
#ParaOptimization.TrueCoordFile /ngsprojects/protist/data_archive/ARTEMIA/trainingSet.aug.txt
ParaOptimization.EvalPredDir ../Procedures/Eval
ParaOptimization.Algorithm GENETIC+LINESEARCH
ParaOptimization.Test 0
ParaOptimization.Trace 1
#
ParaOptimization.NbCluster 15
ParaOptimization.Cluster[0] IDENTICAL
ParaOptimization.Cluster[1] LINKED
ParaOptimization.Cluster[2] LINKED
ParaOptimization.Cluster[3] IDENTICAL
ParaOptimization.Cluster[4] LINKED
ParaOptimization.Cluster[5] LINKED
ParaOptimization.Cluster[6] IDENTICAL
ParaOptimization.Cluster[7] LINKED
ParaOptimization.Cluster[8] LINKED
ParaOptimization.Cluster[9] LINKED
ParaOptimization.Cluster[10] LINKED
ParaOptimization.Cluster[11] LINKED
ParaOptimization.Cluster[12] IDENTICAL
ParaOptimization.Cluster[13] LINKED
ParaOptimization.Cluster[14] LINKED
ParaOptimization.Cluster[15] LINKED
ParaOptimization.Cluster[16] LINKED
ParaOptimization.Cluster[17] IDENTICAL
ParaOptimization.Cluster[18] IDENTICAL
ParaOptimization.Cluster[19] LINKED
ParaOptimization.Cluster[20] LINKED
ParaOptimization.Cluster[21] IDENTICAL
ParaOptimization.Cluster[22] LINKED
ParaOptimization.Cluster[23] LINKED
ParaOptimization.Cluster[24] IDENTICAL
ParaOptimization.Cluster[25] LINKED
ParaOptimization.Cluster[26] LINKED
ParaOptimization.Cluster[27] LINKED
ParaOptimization.Cluster[28] LINKED
ParaOptimization.Cluster[29] LINKED
ParaOptimization.Cluster[30] IDENTICAL
ParaOptimization.Cluster[31] LINKED
ParaOptimization.Cluster[32] LINKED
#
#
ParaOptimization.NbParameter 23
#
ParaOptimization.Para.Name[0] Repeat.ExonPenalty*
ParaOptimization.Para.Max[0] 100
ParaOptimization.Para.Min[0] -5
ParaOptimization.Para.Cluster[0] 0
#
ParaOptimization.Para.Name[1] SMachine.donB*
ParaOptimization.Para.Max[1] 10
ParaOptimization.Para.Min[1] -100
ParaOptimization.Para.Cluster[1] 1
#
ParaOptimization.Para.Name[2] SMachine.donP*
ParaOptimization.Para.Max[2] 1
ParaOptimization.Para.Min[2] -25
ParaOptimization.Para.Cluster[2] 1
#
ParaOptimization.Para.Name[3] SMachine.accB*
ParaOptimization.Para.Max[3] 50
ParaOptimization.Para.Min[3] -5
ParaOptimization.Para.Cluster[3] 2
#
ParaOptimization.Para.Name[4] SMachine.accP*
ParaOptimization.Para.Max[4] 7
ParaOptimization.Para.Min[4] -50
ParaOptimization.Para.Cluster[4] 2
#
ParaOptimization.Para.Name[5] SMachine.tSpliceB*
ParaOptimization.Para.Max[5] 100
ParaOptimization.Para.Min[5] -20
ParaOptimization.Para.Cluster[5] 3
#
ParaOptimization.Para.Name[6] Transcript.Stop*
ParaOptimization.Para.Max[6] 70
ParaOptimization.Para.Min[6] -50
ParaOptimization.Para.Cluster[6] 4
#
ParaOptimization.Para.Name[7] Transcript.Start*
ParaOptimization.Para.Max[7] 3
ParaOptimization.Para.Min[7] -50
ParaOptimization.Para.Cluster[7] 4
#
ParaOptimization.Para.Name[8] Transcript.StopNpc*
ParaOptimization.Para.Max[8] 3
ParaOptimization.Para.Min[8] -50
ParaOptimization.Para.Cluster[8] 5
#
ParaOptimization.Para.Name[9] Transcript.StartNpc*
ParaOptimization.Para.Max[9] 3
ParaOptimization.Para.Min[9] -30
ParaOptimization.Para.Cluster[9] 5
#
ParaOptimization.Para.Name[10] EuStop.stopP*
ParaOptimization.Para.Max[10] 100
ParaOptimization.Para.Min[10] -30
ParaOptimization.Para.Cluster[10] 6
#
ParaOptimization.Para.Name[11] PatConst.patP*[0]
ParaOptimization.Para.Max[11] 10
ParaOptimization.Para.Min[11] -15
ParaOptimization.Para.Cluster[11] 7
#
ParaOptimization.Para.Name[12] PatConst.patPNo*[0]
ParaOptimization.Para.Max[12] 10
ParaOptimization.Para.Min[12] -10
ParaOptimization.Para.Cluster[12] 7
#
ParaOptimization.Para.Name[13] PatConst.patP*[1]
ParaOptimization.Para.Max[13] 5
ParaOptimization.Para.Min[13] -25
ParaOptimization.Para.Cluster[13] 8
#
ParaOptimization.Para.Name[14] PatConst.patPNo*[1]
ParaOptimization.Para.Max[14] 5
ParaOptimization.Para.Min[14] -5
ParaOptimization.Para.Cluster[14] 8
#
ParaOptimization.Para.Name[15] PatConst.patP*[2]
ParaOptimization.Para.Max[15] 2
ParaOptimization.Para.Min[15] -25
ParaOptimization.Para.Cluster[15] 9
#
ParaOptimization.Para.Name[16] PatConst.patPNo*[2]
ParaOptimization.Para.Max[16] 25
ParaOptimization.Para.Min[16] 5
ParaOptimization.Para.Cluster[16] 9
#
ParaOptimization.Para.Name[17] PatConst.patP*[3]
ParaOptimization.Para.Max[17] 5
ParaOptimization.Para.Min[17] -5
ParaOptimization.Para.Cluster[17] 10
#
ParaOptimization.Para.Name[18] PatConst.patPNo*[3]
ParaOptimization.Para.Max[18] 25
ParaOptimization.Para.Min[18] -5
ParaOptimization.Para.Cluster[18] 10
#
#
#
#
#
ParaOptimization.Para.Name[19] Est.estP*[0]
ParaOptimization.Para.Max[19] 0
ParaOptimization.Para.Min[19] -1000000
ParaOptimization.Para.Cluster[19] 11
#
ParaOptimization.Para.Name[20] Est.utrP*[0]
ParaOptimization.Para.Max[20] 20
ParaOptimization.Para.Min[20] -10
ParaOptimization.Para.Cluster[20] 12
#
ParaOptimization.Para.Name[21] Est.CdsBoost*[0]
ParaOptimization.Para.Max[21] 20
ParaOptimization.Para.Min[21] 0
ParaOptimization.Para.Cluster[21] 13
#
ParaOptimization.Para.Name[22] Est.SpliceBoost*[0]
ParaOptimization.Para.Max[22] 100
ParaOptimization.Para.Min[22] 20
ParaOptimization.Para.Cluster[22] 14
#
#
ParaOptimization.Para.Name[23] BlastX.level0*
ParaOptimization.Para.Max[23] 75
ParaOptimization.Para.Min[23] 0
ParaOptimization.Para.Cluster[23] 15
#
ParaOptimization.Para.Name[24] BlastX.level1*
ParaOptimization.Para.Max[24] 10
ParaOptimization.Para.Min[24] 0
ParaOptimization.Para.Cluster[24] 16
#
ParaOptimization.Para.Name[25] BlastX.level2*
ParaOptimization.Para.Max[25] 10
ParaOptimization.Para.Min[25] -30
ParaOptimization.Para.Cluster[25] 17
#
ParaOptimization.Para.Name[26] BlastX.level3*
ParaOptimization.Para.Max[26] 50
ParaOptimization.Para.Min[26] -1
ParaOptimization.Para.Cluster[26] 18
#
ParaOptimization.Para.Name[27] BlastX.blastxM*
ParaOptimization.Para.Max[27] 1
ParaOptimization.Para.Min[27] -50
ParaOptimization.Para.Cluster[27] 19
#
ParaOptimization.Para.Name[28] Est.estP*[1]
ParaOptimization.Para.Max[28] 0
ParaOptimization.Para.Min[28] -10000
ParaOptimization.Para.Cluster[28] 20
#
ParaOptimization.Para.Name[29] Est.utrP*[1]
ParaOptimization.Para.Max[29] 10
ParaOptimization.Para.Min[29] -20
ParaOptimization.Para.Cluster[29] 21
#
ParaOptimization.Para.Name[30] Est.CdsBoost*[1]
ParaOptimization.Para.Max[30] 50
ParaOptimization.Para.Min[30] 0
ParaOptimization.Para.Cluster[30] 22
#
ParaOptimization.Para.Name[31] Est.SpliceBoost*[1]
ParaOptimization.Para.Max[31] 10
ParaOptimization.Para.Min[31] -10
ParaOptimization.Para.Cluster[31] 23
#
ParaOptimization.Para.Name[32] Est.estP*[2]
ParaOptimization.Para.Max[32] 100
ParaOptimization.Para.Min[32] -10000
ParaOptimization.Para.Cluster[32] 24
#
ParaOptimization.Para.Name[33] Est.utrP*[2]
ParaOptimization.Para.Max[33] 40
ParaOptimization.Para.Min[33] -10
ParaOptimization.Para.Cluster[33] 25
#
ParaOptimization.Para.Name[34] Est.CdsBoost*[2]
ParaOptimization.Para.Max[34] 10
ParaOptimization.Para.Min[34] -20
ParaOptimization.Para.Cluster[34] 26
#
ParaOptimization.Para.Name[35] Est.SpliceBoost*[2]
ParaOptimization.Para.Max[35] 20
ParaOptimization.Para.Min[35] -1
ParaOptimization.Para.Cluster[35] 27
#
ParaOptimization.Para.Name[36] Est.estP*[3]
ParaOptimization.Para.Max[36] 0
ParaOptimization.Para.Min[36] -10000
ParaOptimization.Para.Cluster[36] 28
#
ParaOptimization.Para.Name[37] Est.utrP*[3]
ParaOptimization.Para.Max[37] 20
ParaOptimization.Para.Min[37] -10
ParaOptimization.Para.Cluster[37] 29
#
ParaOptimization.Para.Name[38] Est.CdsBoost*[3]
ParaOptimization.Para.Max[38] 10
ParaOptimization.Para.Min[38] -10
ParaOptimization.Para.Cluster[38] 30
#
ParaOptimization.Para.Name[39] Est.SpliceBoost*[3]
ParaOptimization.Para.Max[39] 10
ParaOptimization.Para.Min[39] 0
ParaOptimization.Para.Cluster[39] 31
#
ParaOptimization.Para.Name[40] AnnotaStruct.CDS*[0]
ParaOptimization.Para.Max[40] 1000
ParaOptimization.Para.Min[40] -10000
ParaOptimization.Para.Cluster[40] 32
#
#
################## Genetic ######################################
Genetic.NbRun 2
Genetic.NbGeneration 15
Genetic.NbElement 30
Genetic.CrossOverProbability 0.6
Genetic.MutationProbability 0.2
Genetic.SelectionType 1
#				  1:stochastic remainder without replacement
Genetic.ScalingType 1
#				  1: Sigma Truncation scaling 
#				  2: Power Law scaling
Genetic.Sharing 0.9
#				  1: sharing, looking for clusters which best 
#				     elt fitness is at least n% of the overall 
#	                             best element of the population
Genetic.Clustering 1
Genetic.Elitism 0.9
#				  n: elitism; keeps the best elt if no sharing,
#	                             and keeps the best elt of each cluster 
#				     which best_elt fitness is at
#	                             least n% of the overallbest elt if sharing
Genetic.SA.Mutation 0
Genetic.SA.CrossOver 0
Genetic.Seed 4
#
#
######### LINESEARCH ###########################################
LineSearch.NbMaxCycle 10
LineSearch.NbMinCycle 2
LineSearch.NbMaxStab 2
LineSearch.DivInter 4
LineSearch.Alpha 0.6
LineSearch.EvolutionMini 0.001
LineSearch.Seed 1
#
LineSearch.Para.Step[0] 0.01
LineSearch.Para.Init[0] 4
LineSearch.Para.MaxInit[0] 6
LineSearch.Para.MinInit[0] 3
#
LineSearch.Para.Step[1] 0.01
LineSearch.Para.Init[1] 1
LineSearch.Para.MaxInit[1] 2
LineSearch.Para.MinInit[1] 0
#
LineSearch.Para.Step[2] 0.01
LineSearch.Para.Init[2] 5
LineSearch.Para.MaxInit[2] 10
LineSearch.Para.MinInit[2] 0
#
LineSearch.Para.Step[3] 0.01
LineSearch.Para.Init[3] 0.5
LineSearch.Para.MaxInit[3] 2
LineSearch.Para.MinInit[3] 0
#
LineSearch.Para.Step[4]	0.01
LineSearch.Para.Init[4] 20
LineSearch.Para.MaxInit[4] 40
LineSearch.Para.MinInit[4] 0
#
LineSearch.Para.Step[5]	0.01
LineSearch.Para.Init[5] 4.5
LineSearch.Para.MaxInit[5] 6
LineSearch.Para.MinInit[5] 3
#
LineSearch.Para.Step[6]	0.01
LineSearch.Para.Init[6] 4.5
LineSearch.Para.MaxInit[6] 6
LineSearch.Para.MinInit[6] 3
#
LineSearch.Para.Step[7]	1
LineSearch.Para.Init[7] -5
LineSearch.Para.MaxInit[7] 20
LineSearch.Para.MinInit[7] -30
#
LineSearch.Para.Step[8]	0.01
LineSearch.Para.Init[8] 0
LineSearch.Para.MaxInit[8] 5
LineSearch.Para.MinInit[8] -5
#
LineSearch.Para.Step[9]	1
LineSearch.Para.Init[9] 0
LineSearch.Para.MaxInit[9] 10
LineSearch.Para.MinInit[9] -10
#
LineSearch.Para.Step[10] 0.01
LineSearch.Para.Init[10] 0
LineSearch.Para.MaxInit[10] 5
LineSearch.Para.MinInit[10] -5
#
LineSearch.Para.Step[11] 0.01
LineSearch.Para.Init[11] -0.01
LineSearch.Para.MaxInit[11] -0.1
LineSearch.Para.MinInit[11] -1e4
#
LineSearch.Para.Step[12] 0.01
LineSearch.Para.Init[12] 0.3
LineSearch.Para.MaxInit[12] 0.5
LineSearch.Para.MinInit[12] 0.1
#
LineSearch.Para.Step[13] 0.01
LineSearch.Para.Init[13] 0.5
LineSearch.Para.MaxInit[13] 1
LineSearch.Para.MinInit[13] 0
#
LineSearch.Para.Step[14] 0.01
LineSearch.Para.Init[14] 0.5
LineSearch.Para.MaxInit[14] 1
LineSearch.Para.MinInit[14] 0
#
LineSearch.Para.Step[15] 0.01
LineSearch.Para.Init[15] 0.5
LineSearch.Para.MaxInit[15] 1
LineSearch.Para.MinInit[15] 0
#
LineSearch.Para.Step[16] 0.01
LineSearch.Para.Init[16] 0.5
LineSearch.Para.MaxInit[16] 1
LineSearch.Para.MinInit[16] 0
#
LineSearch.Para.Step[17] 0.01
LineSearch.Para.Init[17] 0.5
LineSearch.Para.MaxInit[17] 1
LineSearch.Para.MinInit[17] 0
#
LineSearch.Para.Step[18] 0.01
LineSearch.Para.Init[18] 0.5
LineSearch.Para.MaxInit[18] 1
LineSearch.Para.MinInit[18] 0
#
LineSearch.Para.Step[19] 0.01
LineSearch.Para.Init[19] 0.5
LineSearch.Para.MaxInit[19] 1
LineSearch.Para.MinInit[19] 0
#
LineSearch.Para.Step[20] 0.01
LineSearch.Para.Init[20] 0.5
LineSearch.Para.MaxInit[20] 1
LineSearch.Para.MinInit[20] 0
#
LineSearch.Para.Step[21] 0.01
LineSearch.Para.Init[21] 0.5
LineSearch.Para.MaxInit[21] 1
LineSearch.Para.MinInit[21] 0
#
LineSearch.Para.Step[22] 0.01
LineSearch.Para.Init[22] 0.5
LineSearch.Para.MaxInit[22] 1
LineSearch.Para.MinInit[22] 0
#
LineSearch.Para.Step[23] 0.01
LineSearch.Para.Init[23] 0.5
LineSearch.Para.MaxInit[23] 1
LineSearch.Para.MinInit[23] 0
#
LineSearch.Para.Step[24] 0.01
LineSearch.Para.Init[24] 0.5
LineSearch.Para.MaxInit[24] 1
LineSearch.Para.MinInit[24] 0
#
LineSearch.Para.Step[25] 0.01
LineSearch.Para.Init[25] 0.5
LineSearch.Para.MaxInit[25] 1
LineSearch.Para.MinInit[25] 0
#
LineSearch.Para.Step[26] 0.01
LineSearch.Para.Init[26] 0.5
LineSearch.Para.MaxInit[26] 1
LineSearch.Para.MinInit[26] 0
#
LineSearch.Para.Step[27] 0.01
LineSearch.Para.Init[27] 0.5
LineSearch.Para.MaxInit[27] 1
LineSearch.Para.MinInit[27] 0
#
LineSearch.Para.Step[28] 0.01
LineSearch.Para.Init[28] 0.5
LineSearch.Para.MaxInit[28] 1
LineSearch.Para.MinInit[28] 0
#
LineSearch.Para.Step[29] 0.01
LineSearch.Para.Init[29] 0.5
LineSearch.Para.MaxInit[29] 1
LineSearch.Para.MinInit[29] 0
#
LineSearch.Para.Step[30] 0.01
LineSearch.Para.Init[30] 0.5
LineSearch.Para.MaxInit[30] 1
LineSearch.Para.MinInit[30] 0
#
LineSearch.Para.Step[31] 0.01
LineSearch.Para.Init[31] 0.5
LineSearch.Para.MaxInit[31] 1
LineSearch.Para.MinInit[31] 0
#
LineSearch.Para.Step[32] 0.01
LineSearch.Para.Init[32] 0.5
LineSearch.Para.MaxInit[32] 1
LineSearch.Para.MinInit[32] 0
#
LineSearch.Para.Step[33] 0.01
LineSearch.Para.Init[33] 0.5
LineSearch.Para.MaxInit[33] 1
LineSearch.Para.MinInit[33] 0
#
LineSearch.Para.Step[34] 0.01
LineSearch.Para.Init[34] 0.5
LineSearch.Para.MaxInit[34] 1
LineSearch.Para.MinInit[34] 0
#
LineSearch.Para.Step[35] 0.01
LineSearch.Para.Init[35] 0.5
LineSearch.Para.MaxInit[35] 1
LineSearch.Para.MinInit[35] 0
#
LineSearch.Para.Step[36] 0.01
LineSearch.Para.Init[36] 0.5
LineSearch.Para.MaxInit[36] 1
LineSearch.Para.MinInit[36] 0
#
LineSearch.Para.Step[37] 0.01
LineSearch.Para.Init[37] 0.5
LineSearch.Para.MaxInit[37] 1
LineSearch.Para.MinInit[37] 0
#
LineSearch.Para.Step[38] 0.01
LineSearch.Para.Init[38] 0.5
LineSearch.Para.MaxInit[38] 1
LineSearch.Para.MinInit[38] 0
#
LineSearch.Para.Step[39] 0.01
LineSearch.Para.Init[39] 0.5
LineSearch.Para.MaxInit[39] 1
LineSearch.Para.MinInit[39] 0
#
LineSearch.Para.Step[40] 0.01
LineSearch.Para.Init[40] 0.5
LineSearch.Para.MaxInit[40] 1
LineSearch.Para.MinInit[40] 0