%0 Journal Article %1 Schaller2021-vf %A Schaller, David %A Hellmuth, Marc %A Stadler, Peter F %D 2021 %I Springer Science and Business Media LLC %J Algorithms Mol. Biol. %K Compatibility Mathematical Rooted of phylogenetics; rooted trees trees; %N 1 %P 23 %R 10.1186/s13015-021-00202-8 %T A simpler linear-time algorithm for the common refinement of rooted phylogenetic trees on a common leaf set %V 16 %X 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 .

@article{Schaller2021-vf, 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 .}, added-at = {2024-09-10T11:54:51.000+0200}, author = {Schaller, David and Hellmuth, Marc and Stadler, Peter F}, biburl = {https://puma.scadsai.uni-leipzig.de/bibtex/207b4b50af12d7929722e02a7fab89220/scadsfct}, copyright = {https://creativecommons.org/licenses/by/4.0}, doi = {10.1186/s13015-021-00202-8}, interhash = {8a3d83100e66e4e828b59a2e03bac9c0}, intrahash = {07b4b50af12d7929722e02a7fab89220}, journal = {Algorithms Mol. Biol.}, keywords = {Compatibility Mathematical Rooted of phylogenetics; rooted trees trees;}, language = {en}, month = dec, number = 1, pages = 23, publisher = {Springer Science and Business Media LLC}, timestamp = {2024-09-10T11:54:51.000+0200}, title = {A simpler linear-time algorithm for the common refinement of rooted phylogenetic trees on a common leaf set}, volume = 16, year = 2021 }