Name
Abstract | ||
|---|---|---|
Abstract Background Tree reconciliation problems have long been studied in phylogenetics. A particular variant of the reconciliation problem for a gene tree T and a species tree S assumes that for each interior vertex x of T it is known whether x represents a speciation or a duplication. This problem appears in the context of analyzing orthology data. Results We show that S is a species tree for T if and only if S displays all rooted triples of T that have three distinct species as their leaves and are rooted in a speciation vertex. A valid reconciliation map can then be found in polynomial time. Simulated data shows that the event-labeled gene trees convey a large amount of information on underlying species trees, even for a large percentage of losses. Conclusions The knowledge of event labels in a gene tree strongly constrains the possible species tree and, for a given species tree, also the possible reconciliation maps. Nevertheless, many degrees of freedom remain in the space of feasible solutions. In order to disambiguate the alternative solutions additional external constraints as well as optimization criteria could be employed. |
Year | DOI | Venue |
|---|---|---|
2012 | 10.1186/1471-2105-13-S19-S6 | BMC Bioinformatics |
Keywords | Field | DocType |
algorithms,microarrays,bioinformatics,biomedical research | Phylogenetic tree,Gene,Vertex (geometry),Biology,Tree rearrangement,K-ary tree,Bioinformatics,Phylogenetics,Gene duplication | Journal |
Volume | Issue | ISSN |
13 | S-19 | 1471-2105 |
Citations | PageRank | References |
22 | 1.03 | 28 |
Authors | ||
6 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Maribel Hernandez-Rosales | 1 | 47 | 3.44 |
| marc hellmuth | 2 | 148 | 22.80 |
| Nicolas Wieseke | 3 | 114 | 9.34 |
| Katharina T. Huber | 4 | 139 | 24.31 |
| Vincent Moulton | 5 | 330 | 48.01 |
| Peter F. Stadler | 6 | 1839 | 152.96 |