| Class Summary | 
| DistanceCalculator |  | 
| DoRIO |  | 
| Int |  | 
| NameAndValues |  | 
| OE | Implements Oliver Eulenstein's algorithm for speciation - duplication inference. | 
| RIO |  | 
| SDI | Abstract class from with classes SDIse and OE inherit. | 
| SDIdirectory | Allows to infer duplications - speciations on all (rooted or unrooted) gene trees in
a directory by using method "infer" of class SDIunrooted. | 
| SDIse | Implements our algorithm for speciation - duplication inference (SDI). | 
| SDIunrooted | Allows to infer duplications - speciations on a unrooted gene tree. | 
| testNHX |  | 
| transfersBranchLenghts |  |