COG 95672 SWG Normalized Score No Cut TM10 TP6 with Sammon

Description

DataSet: COG Size: 95672 Unique: Yes
Aligner: SmithWaterman ScoringMatrix: BLOSUM62 GapOpen: -9 GapExt: -1
DistanceType: Normalized SWG Score (2*AB/AA+BB) Transformation: TM10,TP6
Mapping: Sammon DistanceCut: None
Initialization: Random
Fixed: None
Varied: All
DensitySat: 0.85

Links

• Simple Points
• Colon Points
• Group Points
• Summary File
• Timing File
• Manxcat Output
• Density Graph
• Density Graph for Selected Clusters (Intra Cluster Distances)
• Density Graph for Selected Clusters (Inter Cluster Distances)
• PlotViz

Images

Full Sample with Selected Clusters

Full Sample with Selected Clusters Zoomed-in

Configuration

I/O
 CoordinateWriteFrequency:      0
 DistanceMatrixFile:            F:\Salsa\saliya\cog\100k\input\cog_95672_swg_distance_normscore_c#.bin


ManxcatCore
 AddonforQcomputation:          2
 CalcFixedCrossFixed:           True
 CGResidualLimit:               1E-05
 ChisqChangePerPoint:           0.001
 Chisqnorm:                     2
 ChisqPrintConstant:            1
 ConversionInformation:         
 ConversionOption:              
 DataPoints:                    95672
 Derivtest:                     False
 DiskDistanceOption:            2
 DistanceCut:                   -1
 DistanceFormula:               1
 DistanceProcessingOption:      0
 DistanceWeigthsCuts:           
 Eigenvaluechange:              0.001
 Eigenvectorchange:             0.001
 ExtraOption1:                  0
 Extraprecision:                0.05
 FixedPointCriterion:           none
 FletcherRho:                   0.25
 FletcherSigma:                 0.75
 FullSecondDerivativeOption:    0
 FunctionErrorCalcMultiplier:   10
 HistogramBinCount              100
 InitializationLoops:           2
 InitializationOption:          0
 InitialSteepestDescents:       0
 LinkCut:                       5
 LocalVectorDimension:          3
 Maxit:                         120
 MinimumDistance:               -0.001
 MPIIOStrategy:                 0
 Nbadgo:                        6
 Omega:                         1.25
 OmegaOption:                   0
 PowerIterationLimit:           200
 ProcessingOption:              0
 QgoodReductionFactor:          0.5
 QHighInitialFactor:            0.01
 QLimiscalecalculationInterval: 1
 RotationOption:                0
 Selectedfixedpoints:           
 Selectedvariedpoints:          
 StoredDistanceOption:          2
 TimeCutmillisec:               -1
 TransformMethod:               10
 TransformParameter:            6
 UndefindDistanceValue:         -1
 VariedPointCriterion:          all
 WeightingOption:               0
 Write2Das3D:                   True


Density
 Alpha:                         2
 Pcutf:                         0.85
 SelectedClusters:              63,82,145,265,362,684,708
 XmaxBound:                     1.5
 Xres:                          50
 YmaxBound:                     1.5
 Yres:                          50

COG 95672 SWG Normalized Score TM10 TP6 with Sammon

Description

DataSet: COG Size: 95672 Unique: Yes
Aligner: SmithWaterman ScoringMatrix: BLOSUM62 GapOpen: -9 GapExt: -1
DistanceType: Normalized SWG Score (2*AB/AA+BB) Transformation: TM10,TP6
Mapping: Sammon DistanceCut: 0.96
Initialization: Random
Fixed: None
Varied: All
DensitySat: 0.85

Links

• Simple Points
• Colon Points
• Group Points
• Summary File
• Timing File
• Manxcat Output
• Density Graph
• Density Graph for Selected Clusters (Intra Cluster Distances)
• Density Graph for Selected Clusters (Inter Cluster Distances)
• PlotViz

Images

Full Sample with Selected Clusters Zoomed-in

Configuration

I/O
 CoordinateWriteFrequency:      0
 DistanceMatrixFile:            F:\Salsa\saliya\cog\100k\input\cog_95672_swg_distance_normscore_c#.bin


ManxcatCore
 AddonforQcomputation:          2
 CalcFixedCrossFixed:           True
 CGResidualLimit:               1E-05
 ChisqChangePerPoint:           0.001
 Chisqnorm:                     2
 ChisqPrintConstant:            1
 ConversionInformation:         
 ConversionOption:              
 DataPoints:                    95672
 Derivtest:                     False
 DiskDistanceOption:            2
 DistanceCut:                   0.96
 DistanceFormula:               1
 DistanceProcessingOption:      0
 DistanceWeigthsCuts:           
 Eigenvaluechange:              0.001
 Eigenvectorchange:             0.001
 ExtraOption1:                  0
 Extraprecision:                0.05
 FixedPointCriterion:           none
 FletcherRho:                   0.25
 FletcherSigma:                 0.75
 FullSecondDerivativeOption:    0
 FunctionErrorCalcMultiplier:   10
 HistogramBinCount              100
 InitializationLoops:           2
 InitializationOption:          0
 InitialSteepestDescents:       0
 LinkCut:                       5
 LocalVectorDimension:          3
 Maxit:                         120
 MinimumDistance:               -0.001
 MPIIOStrategy:                 0
 Nbadgo:                        6
 Omega:                         1.25
 OmegaOption:                   0
 PowerIterationLimit:           200
 ProcessingOption:              0
 QgoodReductionFactor:          0.5
 QHighInitialFactor:            0.01
 QLimiscalecalculationInterval: 1
 RotationOption:                0
 Selectedfixedpoints:           
 Selectedvariedpoints:          
 StoredDistanceOption:          2
 TimeCutmillisec:               -1
 TransformMethod:               10
 TransformParameter:            6
 UndefindDistanceValue:         -1
 VariedPointCriterion:          all
 WeightingOption:               0
 Write2Das3D:                   True


Density
 Alpha:                         2
 Pcutf:                         0.85
 SelectedClusters:              63,82,145,265,362,684,708
 XmaxBound:                     1
 Xres:                          50
 YmaxBound:                     1
 Yres:                          50

COG 95672 Blast TM10 TP6 with Sammon

Description

DataSet: COG Size: 95672 Unique: Yes
Aligner: Blast ScoringMatrix: BLOSUM62 GapOpen: -16 GapExt: -4
DistanceType: Normalized BitScore (2*AB/AA+BB) Transformation: TM10,TP6
Mapping: Sammon DistanceCut: 0.96
Initialization: Random
Fixed: None
Varied: All
DensitySat: 0.85

Links

• Simple Points
• Colon Points
• Group Points
• Summary File
• Timing File
• Manxcat Output
• Density Graph
• Density Graph for Selected Clusters (Intra Cluster Distances)
• Density Graph for Selected Clusters (Inter Cluster Distances)
• PlotViz

Images

Full Sample with Selected Clusters

Full Sample with Selected Clusters Zoomed-in

Configuration

I/O
 CoordinateWriteFrequency:      0
 DistanceMatrixFile:            F:\Salsa\saliya\cog\100k\input\cog_95672_bitscore_refined_c#.bin


ManxcatCore
 AddonforQcomputation:          2
 CalcFixedCrossFixed:           True
 CGResidualLimit:               1E-05
 ChisqChangePerPoint:           0.001
 Chisqnorm:                     2
 ChisqPrintConstant:            1
 ConversionInformation:         
 ConversionOption:              
 DataPoints:                    95672
 Derivtest:                     False
 DiskDistanceOption:            2
 DistanceCut:                   0.96
 DistanceFormula:               1
 DistanceProcessingOption:      0
 DistanceWeigthsCuts:           
 Eigenvaluechange:              0.001
 Eigenvectorchange:             0.001
 ExtraOption1:                  0
 Extraprecision:                0.05
 FixedPointCriterion:           none
 FletcherRho:                   0.25
 FletcherSigma:                 0.75
 FullSecondDerivativeOption:    0
 FunctionErrorCalcMultiplier:   10
 HistogramBinCount              100
 InitializationLoops:           1
 InitializationOption:          1
 InitialSteepestDescents:       0
 LinkCut:                       5
 LocalVectorDimension:          3
 Maxit:                         80
 MinimumDistance:               -0.001
 MPIIOStrategy:                 0
 Nbadgo:                        6
 Omega:                         1.25
 OmegaOption:                   0
 PowerIterationLimit:           200
 ProcessingOption:              100
 QgoodReductionFactor:          0.5
 QHighInitialFactor:            0.01
 QLimiscalecalculationInterval: 1
 RotationOption:                0
 Selectedfixedpoints:           
 Selectedvariedpoints:          
 StoredDistanceOption:          2
 TimeCutmillisec:               -1
 TransformMethod:               10
 TransformParameter:            6
 UndefindDistanceValue:         -1
 VariedPointCriterion:          all
 WeightingOption:               0
 Write2Das3D:                   True


Density
 Alpha:                         2
 Pcutf:                         0.85
 SelectedClusters:              63,82,145,265,362,684,708
 XmaxBound:                     1.8
 Xres:                          50
 YmaxBound:                     1.8
 Yres:                          50