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Time-consistent reconciliation maps and forbidden time travel

Overview of attention for article published in Algorithms for Molecular Biology, February 2018
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Title
Time-consistent reconciliation maps and forbidden time travel
Published in
Algorithms for Molecular Biology, February 2018
DOI 10.1186/s13015-018-0121-8
Pubmed ID
Authors

Nikolai Nøjgaard, Manuela Geiß, Daniel Merkle, Peter F. Stadler, Nicolas Wieseke, Marc Hellmuth

Abstract

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 toevent-labeledgene trees. Knowledge of the event labels considerably simplifies the problem of reconciling a gene treeTwith a species treesS, 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. 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 [Formula: see text]-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. The combinatorial characterization of time consistency and thus biologically feasible reconciliation is an important step towards the inference of gene family histories with horizontal 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.

Twitter Demographics

The data shown below were collected from the profiles of 3 tweeters who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 10 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 10 100%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 3 30%
Student > Bachelor 3 30%
Student > Doctoral Student 1 10%
Researcher 1 10%
Professor > Associate Professor 1 10%
Other 0 0%
Unknown 1 10%
Readers by discipline Count As %
Computer Science 4 40%
Engineering 2 20%
Biochemistry, Genetics and Molecular Biology 1 10%
Mathematics 1 10%
Unknown 2 20%

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 13 November 2018.
All research outputs
#10,502,450
of 13,786,654 outputs
Outputs from Algorithms for Molecular Biology
#132
of 208 outputs
Outputs of similar age
#237,619
of 355,771 outputs
Outputs of similar age from Algorithms for Molecular Biology
#1
of 1 outputs
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