| Class | Description |
|---|---|
| AMatrixPlugin | |
| AddDistanceMatrixPlugin | |
| DistanceMatrixPlugin | |
| DistanceMatrixRangesPlugin | |
| DominanceNormalizedIBSMatrix | |
| DominanceRelationshipMatrix |
Compute Dominance Relationship Matrix for all pairs of taxa. Missing sites are ignored. http://www.genetics.org/content/198/4/1759.abstract
|
| EndelmanDistanceMatrix | |
| GCTADistanceMatrix | |
| HMatrixPlugin | |
| IBSDistanceMatrix |
This class calculates an identity by state matrix. It is scaled so only non-missing comparison are used. It conducts bit level calculations of IBS for genotypes. Only the two most common alleles are used in the distance calculations.
|
| IBSDistanceMatrix2Alleles | |
| IBSDistanceMatrix3Alleles | |
| IBSDistanceMatrixOneByAll | |
| Kinship | Deprecated |
| KinshipPlugin | |
| MultiDimensionalScalingPlugin | |
| RemoveNaNFromDistanceMatrixPlugin | |
| SubtractDistanceMatrixPlugin | |
| VCAPScanPlugin |