Efficiently sparse listing of classes of optimal cophylogeny reconciliations - Inria - Institut national de recherche en sciences et technologies du numérique Access content directly
Journal Articles Algorithms for Molecular Biology Year : 2022

Efficiently sparse listing of classes of optimal cophylogeny reconciliations


Background : Cophylogeny reconciliation is a powerful method for analyzing host-parasite (or host-symbiont) co-evolution. It models co-evolution as an optimization problem where the set of all optimal solutions may represent different biological scenarios which thus need to be analyzed separately. Despite the significant research done in the area, few approaches have addressed the problem of helping the biologist deal with the often huge space of optimal solutions. Results : In this paper, we propose a new approach to tackle this problem. We introduce three different criteria under which two solutions may be considered biologically equivalent, and then we propose polynomial-delay algorithms that enumerate only one representative per equivalence class (without listing all the solutions). Conclusions : Our results are of both theoretical and practical importance. Indeed, as shown by the experiments, we are able to significantly reduce the space of optimal solutions while still maintaining important biological information about the whole space.
Fichier principal
Vignette du fichier
wang2022.pdf (1.97 Mo) Télécharger le fichier
Origin : Publisher files allowed on an open archive

Dates and versions

hal-03576371 , version 1 (16-02-2022)





Yishu Wang, Marie-France Sagot, Arnaud Mary, Blerina Sinaimeri. Efficiently sparse listing of classes of optimal cophylogeny reconciliations. Algorithms for Molecular Biology, 2022, 17 (1), pp.1-16. ⟨10.1186/s13015-022-00206-y⟩. ⟨hal-03576371⟩
184 View
58 Download



Gmail Facebook X LinkedIn More