| Class | Description |
|---|---|
| DiversityAnalyses |
This method calculated estimates of nucleotide diversity (pi, theta, etc). In order to provide high performance, it establishes one nucleotide SitePattern, and then manipulates the weighting patterns for sliding windows and different types of sites. Total segregating sites needs to be adjusted for missing and gap data, as this will modify Theta and Tajima estimates
|
| DonorHypoth | |
| LDResult |
Container class for reporting LD results. This class could still be expanded to include the two sites with various sort approaches. The reason for this functionality is so that classes can calculate LD for billions of site pairs, but only retain the most significant.
|
| LinkageDiseqDisplayPlugin | |
| LinkageDisequilibrium |
This class calculates D' and r^2 estimates of linkage disequilibrium. It also calculates the significance of the LD by either Fisher Exact or the multinomial permutation test. This class can work with either normal alignments of annotated alignments. The alignments should be stripped of invariable numSites.
|
| LinkageDisequilibriumComponent |
An AWT Component for displaying information on linkage disequilibrium. Nice schematics are produced if an annotation alignment is used to construct LinkageDisequilibrium. It can portray things both on the gene and chromosomal scale.
|
| LinkageDisequilibriumMinimapComponent | |
| LinkageDisequilibriumPlugin | |
| PolymorphismDistribution |
This class provides the distribution of polymorphisms
|
| SequenceDiversityPlugin |