Maximum parsimony distance on phylogenetic trees: A linear kernel and constant factor approximation algorithm: A linear kernel and constant factor approximation algorithm
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| Title: | Maximum parsimony distance on phylogenetic trees: A linear kernel and constant factor approximation algorithm: A linear kernel and constant factor approximation algorithm |
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| Authors: | Leen Stougie, Mark Jones, Steven Kelk |
| Contributors: | Sagot, Marie-France |
| Source: | Journal of Computer and System Sciences. 117:165-181 |
| Publication Status: | Preprint |
| Publisher Information: | Elsevier BV, 2021. |
| Publication Year: | 2021 |
| Subject Terms: | Maximum agreement forest, FOS: Computer and information sciences, COMPLEXITY, 0102 computer and information sciences, [INFO] Computer Science [cs], COMPATIBILITY, 01 natural sciences, [SDV] Life Sciences [q-bio], Phylogenetics, Computer Science - Data Structures and Algorithms, Fixed parameter tractability, Data Structures and Algorithms (cs.DS), Maximum parsimony, AGREEMENT FOREST |
| Description: | Maximum parsimony distance is a measure used to quantify the dissimilarity of two unrooted phylogenetic trees. It is NP-hard to compute, and very few positive algorithmic results are known due to its complex combinatorial structure. Here we address this shortcoming by showing that the problem is fixed parameter tractable. We do this by establishing a linear kernel i.e., that after applying certain reduction rules the resulting instance has size that is bounded by a linear function of the distance. As powerful corollaries to this result we prove that the problem permits a polynomial-time constant-factor approximation algorithm; that the treewidth of a natural auxiliary graph structure encountered in phylogenetics is bounded by a function of the distance; and that the distance is within a constant factor of the size of a maximum agreement forest of the two trees, a well studied object in phylogenetics. 27 pages, 7 figures |
| Document Type: | Article |
| File Description: | application/pdf |
| Language: | English |
| ISSN: | 0022-0000 |
| DOI: | 10.1016/j.jcss.2020.10.003 |
| DOI: | 10.48550/arxiv.2004.02298 |
| Access URL: | http://arxiv.org/abs/2004.02298 https://hdl.handle.net/1871.1/0522f5f0-ab66-4220-84ab-f66b5b6df576 https://doi.org/10.1016/j.jcss.2020.10.003 https://research.vu.nl/en/publications/0522f5f0-ab66-4220-84ab-f66b5b6df576 https://cris.maastrichtuniversity.nl/en/publications/d9294f35-8b17-42ce-a4db-36cabf9c7d63 https://doi.org/10.1016/j.jcss.2020.10.003 https://inria.hal.science/hal-03498430v1 https://doi.org/10.1016/j.jcss.2020.10.003 https://inria.hal.science/hal-03498430v1/document https://ir.cwi.nl/pub/30410 https://repository.tudelft.nl/islandora/object/uuid%3A8d5fc924-a45d-4472-a20c-54d511c45632/datastream/OBJ/download https://research.tudelft.nl/en/publications/maximum-parsimony-distance-on-phylogenetic-trees-a-linear-kernel- https://www.narcis.nl/publication/RecordID/oai%3Acwi.nl%3A30410 https://research.vu.nl/en/publications/maximum-parsimony-distance-on-phylogenetic-trees-a-linear-kernel- https://ir.cwi.nl/pub/30410/30410.pdf http://resolver.tudelft.nl/uuid:8d5fc924-a45d-4472-a20c-54d511c45632 |
| Rights: | CC BY arXiv Non-Exclusive Distribution |
| Accession Number: | edsair.doi.dedup.....677f9b51e4e2d56f977cbdc9757ff034 |
| Database: | OpenAIRE |
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Nájsť tento článok vo Web of Science | Abstract: | Maximum parsimony distance is a measure used to quantify the dissimilarity of two unrooted phylogenetic trees. It is NP-hard to compute, and very few positive algorithmic results are known due to its complex combinatorial structure. Here we address this shortcoming by showing that the problem is fixed parameter tractable. We do this by establishing a linear kernel i.e., that after applying certain reduction rules the resulting instance has size that is bounded by a linear function of the distance. As powerful corollaries to this result we prove that the problem permits a polynomial-time constant-factor approximation algorithm; that the treewidth of a natural auxiliary graph structure encountered in phylogenetics is bounded by a function of the distance; and that the distance is within a constant factor of the size of a maximum agreement forest of the two trees, a well studied object in phylogenetics.<br />27 pages, 7 figures |
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| ISSN: | 00220000 |
| DOI: | 10.1016/j.jcss.2020.10.003 |