1 Search Results for "Geiß, Manuela"

Document
DOI: 10.4230/LIPIcs.WABI.2017.17
Forbidden Time Travel: Characterization of Time-Consistent Tree Reconciliation Maps

Authors: Nikolai Nojgaard, Manuela Geiß, Daniel Merkle, Peter F. Stadler, Nicolas Wieseke, and Marc Hellmuth

Published in: LIPIcs, Volume 88, 17th International Workshop on Algorithms in Bioinformatics (WABI 2017)

Abstract
Motivation: In the absence of horizontal gene transfer it is possible to reconstruct the history of gene families from empirically determined orthology relations, which are equivalent to event-labeled gene trees. Knowledge of the event labels considerably simplifies the problem of reconciling a gene tree T with a species trees S, relative to the reconciliation problem without prior knowledge of the event types. It is well-known that optimal reconciliations in the unlabeled case may violate time-consistency and thus are not biologically feasible. Here we investigate the mathematical structure of the event labeled reconciliation problem with horizontal transfer. Results: We investigate the issue of time-consistency for the event-labeled version of the reconciliation problem, provide a convenient axiomatic framework, and derive a complete characterization of time-consistent reconciliations. This characterization depends on certain weak conditions on the event-labeled gene trees that reflect conditions under which evolutionary events are observable at least in principle. We give an O(|V(T)|log(|V(S)|))-time algorithm to decide whether a time-consistent reconciliation map exists. It does not require the construction of explicit timing maps, but relies entirely on the comparably easy task of checking whether a small auxiliary graph is acyclic. The algorithms are implemented in C++ using the boost graph library and are freely available at https://github.com/Nojgaard/tc-recon. Significance: The combinatorial characterization of time consistency and thus biologically feasible reconciliation is an important step towards the inference of gene family histories with hor- izontal transfer from orthology data, i.e., without presupposed gene and species trees. The fast algorithm to decide time consistency is useful in a broader context because it constitutes an attractive component for all tools that address tree reconciliation problems.
Cite as

Nikolai Nojgaard, Manuela Geiß, Daniel Merkle, Peter F. Stadler, Nicolas Wieseke, and Marc Hellmuth. Forbidden Time Travel: Characterization of Time-Consistent Tree Reconciliation Maps. In 17th International Workshop on Algorithms in Bioinformatics (WABI 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 88, pp. 17:1-17:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)

Copy BibTex To Clipboard

@InProceedings{nojgaard_et_al:LIPIcs.WABI.2017.17,
  author =	{Nojgaard, Nikolai and Gei{\ss}, Manuela and Merkle, Daniel and Stadler, Peter F. and Wieseke, Nicolas and Hellmuth, Marc},
  title =	{{Forbidden Time Travel: Characterization of Time-Consistent Tree Reconciliation Maps}},
  booktitle =	{17th International Workshop on Algorithms in Bioinformatics (WABI 2017)},
  pages =	{17:1--17:12},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-050-7},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{88},
  editor =	{Schwartz, Russell and Reinert, Knut},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2017.17},
  URN =		{urn:nbn:de:0030-drops-76362},
  doi =		{10.4230/LIPIcs.WABI.2017.17},
  annote =	{Keywords: Tree Reconciliation, Horizontal Gene Transfer, Reconciliation Map, Time-Consistency, History of gene families}
}
  • Refine by Author
  • 1 Geiß, Manuela
  • 1 Hellmuth, Marc
  • 1 Merkle, Daniel
  • 1 Nojgaard, Nikolai
  • 1 Stadler, Peter F.
  • Show More...

  • Refine by Classification

  • Refine by Keyword
  • 1 History of gene families
  • 1 Horizontal Gene Transfer
  • 1 Reconciliation Map
  • 1 Time-Consistency
  • 1 Tree Reconciliation

  • Refine by Type
  • 1 document

  • Refine by Publication Year
  • 1 2017

Questions / Remarks / Feedback
X

Feedback for Dagstuhl Publishing


Thanks for your feedback!

Feedback submitted

Could not send message

Please try again later or send an E-mail
© 2023-2024 Schloss Dagstuhl – LZI GmbH Imprint Privacy Contact