Space of gene/species trees reconciliations and parsimonious models
We describe algorithms to study the space of all possible reconciliations between a gene tree and a species tree, that is counting the size of this space, uniformly generate a random reconciliation, and exploring this space in optimal time using combinatorial operators. We also extend these algorith...
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| Veröffentlicht in: | Journal of computational biology 2009-10, Vol.16 (10), p.1399-1418 |
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| container_title | Journal of computational biology |
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| creator | Doyon, Jean-Philippe Chauve, Cedric Hamel, Sylvie |
| description | We describe algorithms to study the space of all possible reconciliations between a gene tree and a species tree, that is counting the size of this space, uniformly generate a random reconciliation, and exploring this space in optimal time using combinatorial operators. We also extend these algorithms for optimal and sub-optimal reconciliations according to the three usual combinatorial costs (duplication, loss, and mutation). Applying these algorithms to simulated and real gene family evolutionary scenarios, we observe that the LCA (Last Common Ancestor) based reconciliation is almost always identical to the real one. |
| doi_str_mv | 10.1089/cmb.2009.0095 |
| format | Article |
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| source | Mary Ann Liebert Online Subscription; MEDLINE; Alma/SFX Local Collection |
| subjects | Algorithms Animals Computational biology Drosophila - classification Drosophila - genetics Evolution, Molecular Gene expression Genetic algorithms Genetic Speciation Genome Humans Models, Genetic Phylogeny |
| title | Space of gene/species trees reconciliations and parsimonious models |
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