COG 183362+4872 NW PID Log(1-d^6) with Sammon

COG 183362+4872 NW PID Log(1-d^6) with Sammon

Description

DataSet: COG Size: 183362+4872 Unique: Yes* (5 from 4872 overlaps with 183362)

Aligner: NeedlemanWunsch ScoringMatrix: BLOSUM62 GapOpen: -9 GapExt: -1

DistanceType: (1 - PercentIdentity) Transformation: TM12,TP6

Mapping: Sammon DistanceCut: None

Initialization: Random

Fixed: None

Varied: All

Links

• Simple Points
• Summary File
• Manxcat Output
• PlotViz

Images

Full Sample with Selected Clusters

Full Sample with Selected Clusters Zoomed-in

Full Sample with Selected Clusters and Consensus

COG 95672 NW PID Log(1-d^4) with Sammon

Description

DataSet: COG Size: 95672 Unique: Yes

Aligner: NeedlemanWunsch ScoringMatrix: BLOSUM62 GapOpen: -16 GapExt: -4

DistanceType: (1 - PercentIdentity) Transformation: TM12,TP4

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

COG 95672 NW PID Log(1-d^2) with Sammon

Description

DataSet: COG Size: 95672 Unique: Yes

Aligner: NeedlemanWunsch ScoringMatrix: BLOSUM62 GapOpen: -16 GapExt: -4

DistanceType: (1 - PercentIdentity) Transformation: TM12,TP2

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

COG 95672 NW PID Log(1-d) with Sammon

Description

DataSet: COG Size: 95672 Unique: Yes
Aligner: NeedlemanWunsch ScoringMatrix: BLOSUM62 GapOpen: -16 GapExt: -4
DistanceType: (1 - PercentIdentity) Transformation: TM12
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

COG 50000 Blast PID TM10 TP4 with Chisq1

Description

DataSet: COG Size: 50000 Unique: Yes
Aligner: Blast ScoringMatrix: BLOSUM62 GapOpen: -16 GapExt: -4
DistanceType: (1 - PercentIdentity) Transformation: TM10,TP4
Mapping: Chisq1 DistanceCut: 0.96
Initialization: Random
Fixed: None
Varied: All
DensitySat: 0.85

Links

• Simple Points
• Colon Points
• Group Points
• Summary File
• Timing File
• Manxcat Ouput
• 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

Configuration

I/O
 CoordinateWriteFrequency:      0
 DistanceMatrixFile:            F:\Salsa\saliya\cog\100k\input\cog_95672_bitscore_refined_first50k_c#.bin


ManxcatCore
 AddonforQcomputation:          2
 CalcFixedCrossFixed:           True
 CGResidualLimit:               1E-05
 ChisqChangePerPoint:           0.001
 Chisqnorm:                     1
 ChisqPrintConstant:            1
 ConversionInformation:         
 ConversionOption:              
 DataPoints:                    50000
 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:            4
 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

COG 95672 SWG PID TM10 TP4 with Sammon

Description

DataSet: COG Size: 95672 Unique: Yes
Aligner: SmithWaterman ScoringMatrix: BLOSUM62 GapOpen: -16 GapExt: -4
DistanceType: (1 - PercentIdentity) Transformation: TM10,TP4
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

Configuration

I/O
 CoordinateWriteFrequency:      0
 DistanceMatrixFile:            F:\Salsa\saliya\cog\100k\input\cog_95672_swg_blosum62_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:           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:            4
 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 NW PID SQRT4D with Sammon

Description

DataSet: COG Size: 95672 Unique: Yes
Aligner: NeedlemanWunsch ScoringMatrix: BLOSUM62 GapOpen: -16 GapExt: -4
DistanceType: (1 - PercentIdentity) Transformation: TM9
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_nw_4d_sqrt_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:           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:               0
 TransformParameter:            0.125
 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 NW PID Untransformed with Sammon

Description

DataSet: COG Size: 95672 Unique: Yes
Aligner: NeedlemanWunsch ScoringMatrix: BLOSUM62 GapOpen: -16 GapExt: -4
DistanceType: (1 - PercentIdentity) Transformation: None
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

Configuration

I/O
 CoordinateWriteFrequency:      0
 DistanceMatrixFile:            F:\Salsa\saliya\cog\100k\input\cog_95672_nw_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:           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:               0
 TransformParameter:            0.125
 UndefindDistanceValue:         -1
 VariedPointCriterion:          all
 WeightingOption:               0
 Write2Das3D:                   True


Density
 Alpha:                         2
 Pcutf:                         0.85
 SelectedClusters:              63,82,145,265,362,684,708
 XmaxBound:                     1.2
 Xres:                          50
 YmaxBound:                     1.2
 Yres:                          50