Correction of Weighted Orthology and Paralogy Relations - Complexity and Algorithmic Results
A relation graph for a gene family is a graph with vertices representing the genes, edges connecting pairs of orthologous genes and “missing” edges representing paralogs. While a gene tree directly leads to a set of orthology and paralogy relations, the converse is not always true. Indeed a relation graph cannot necessarily be inferred from any tree, and even if it is “satisfiable” by a tree, this tree is not necessarily “consistent”, i.e. does not necessarily reflect a valid history for the genes, in agreement with a species tree. Here, we consider the problems of minimally correcting a relation graph for satisfiability and consistency, when a degree of confidence is assigned to each orthology or paralogy relation, leading to a weighted relation graph. We provide complexity and algorithmic results for minimizing corrections on a weighted graph, and also for the maximization variant of the problems for unweighted graphs.
- 5.The Gene Ontology Consortium: Gene ontology: tool for the unification of biology. Nat. Genet. 25(1), 25–29 (2000)Google Scholar
- 10.Hellmuth, M., Wieseke, N., Lechner, M., Lenhof, H.-P., Middendorf, M., Stadler, P.F.: Phylogenomics with paralogs. In: PNAS (2014)Google Scholar
- 11.Hernandez-Rosales, M., Hellmuth, M., Wieseke, N., Huber, K.T., Moulton, V., Stadler, P.F.: From event-labeled gene trees to species trees. BMC Bioinform. 13(Suppl 19), S6 (2012)Google Scholar
- 16.Lafond, M., Swenson, K., El-Mabrouk, N.: Error detection and correction of gene trees. In: Chauve, C., El-Mabrouk, N., Tannier, E. (eds.) Models and Algorithms for Genome Evolution. Springer, London (2013)Google Scholar