Orthology relations, symbolic ultrametrics, and cographs
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Publication:1937881
DOI10.1007/s00285-012-0525-xzbMath1408.05038OpenAlexW2041346050WikidataQ45375976 ScholiaQ45375976MaRDI QIDQ1937881
Maribel Hernandez-Rosales, Peter F. Stadler, Katharina T. Huber, Nicolas Wieseke, Marc Hellmuth, Vincent L. Moulton
Publication date: 1 February 2013
Published in: Journal of Mathematical Biology (Search for Journal in Brave)
Full work available at URL: https://doi.org/10.1007/s00285-012-0525-x
Trees (05C05) Problems related to evolution (92D15) Applications of graph theory (05C90) Graph theory (including graph drawing) in computer science (68R10) Distance in graphs (05C12)
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Uses Software
Cites Work
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- New results on optimizing rooted triplets consistency
- Complement reducible graphs
- Recovering symbolically dated, rooted trees from symbolic ultrametrics
- Constructing a tree from homeomorphic subtrees, with applications to computational evolutionary biology
- A supertree method for rooted trees
- Applying modular decomposition to parameterized cluster editing problems
- Cograph Editing: Complexity and Parameterized Algorithms
- Inferring a Tree from Lowest Common Ancestors with an Application to the Optimization of Relational Expressions