David Schaller1, Marc Hellmuth2, Peter F Stadler3,4,5,6,7,8. 1. Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstraße 16-18, 04107, Leipzig, Germany. 2. Department of Mathematics, Faculty of Science, Stockholm University, SE-10691, Stockholm, Sweden. 3. Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstraße 16-18, 04107, Leipzig, Germany. studla@bioinf.uni-leipzig.de. 4. Competence Center for Scalable Data Services and Solutions Dresden/Leipzig, Interdisciplinary Center for Bioinformatics, German Centre for Integrative Biodiversity Research (iDiv), and Leipzig Research Center for Civilization Diseases, Universität Leipzig, Augustusplatz 12, 04107, Leipzig, Germany. studla@bioinf.uni-leipzig.de. 5. Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, 04109, Leipzig, Germany. studla@bioinf.uni-leipzig.de. 6. Department of Theoretical Chemistry, University of Vienna, Währinger Straße 17, 1090, Vienna, Austria. studla@bioinf.uni-leipzig.de. 7. Facultad de Ciencias, Universidad National de Colombia, Sede Bogotá, Ciudad Universitaria, Bogotá, 111321, D.C, Colombia. studla@bioinf.uni-leipzig.de. 8. Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM, 87501, USA. studla@bioinf.uni-leipzig.de.
Abstract
BACKGROUND: The supertree problem, i.e., the task of finding a common refinement of a set of rooted trees is an important topic in mathematical phylogenetics. The special case of a common leaf set L is known to be solvable in linear time. Existing approaches refine one input tree using information of the others and then test whether the results are isomorphic. RESULTS: An O(k|L|) algorithm, LinCR, for constructing the common refinement T of k input trees with a common leaf set L is proposed that explicitly computes the parent function of T in a bottom-up approach. CONCLUSION: LinCR is simpler to implement than other asymptotically optimal algorithms for the problem and outperforms the alternatives in empirical comparisons. AVAILABILITY: An implementation of LinCR in Python is freely available at https://github.com/david-schaller/tralda .
BACKGROUND: The supertree problem, i.e., the task of finding a common refinement of a set of rooted trees is an important topic in mathematical phylogenetics. The special case of a common leaf set L is known to be solvable in linear time. Existing approaches refine one input tree using information of the others and then test whether the results are isomorphic. RESULTS: An O(k|L|) algorithm, LinCR, for constructing the common refinement T of k input trees with a common leaf set L is proposed that explicitly computes the parent function of T in a bottom-up approach. CONCLUSION: LinCR is simpler to implement than other asymptotically optimal algorithms for the problem and outperforms the alternatives in empirical comparisons. AVAILABILITY: An implementation of LinCR in Python is freely available at https://github.com/david-schaller/tralda .
Authors: Manuela Geiß; Edgar Chávez; Marcos González Laffitte; Alitzel López Sánchez; Bärbel M R Stadler; Dulce I Valdivia; Marc Hellmuth; Maribel Hernández Rosales; Peter F Stadler Journal: J Math Biol Date: 2019-04-09 Impact factor: 2.259
Authors: David Schaller; Manuela Geiß; Edgar Chávez; Marcos González Laffitte; Alitzel López Sánchez; Bärbel M R Stadler; Dulce I Valdivia; Marc Hellmuth; Maribel Hernández Rosales; Peter F Stadler Journal: J Math Biol Date: 2021-04-05 Impact factor: 2.259