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| HyPhy-package | Macroevolutionary phylogentic analysis of species trees and gene trees |
| get.recon.1 | Internal Functions |
| HyPhy | Macroevolutionary phylogentic analysis of species trees and gene trees |
| recon.score | Duplications and losses for gene tree in a species tree |
| requiprobable | Sample trees from an equiprobable labeled, semi-labeled or unlabeled distribution |
| rgenetree | Samples gene family trees that evolved on a species tree with various conditions. |