A Practical Fixed-Parameter Algorithm for Constructing Tree-Child Networks from Multiple Binary Trees
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| Title: | A Practical Fixed-Parameter Algorithm for Constructing Tree-Child Networks from Multiple Binary Trees |
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| Authors: | Leo van Iersel, Remie Janssen, Mark Jones, Yukihiro Murakami, Norbert Zeh |
| Source: | Algorithmica. 84:917-960 |
| Publication Status: | Preprint |
| Publisher Information: | Springer Science and Business Media LLC, 2022. |
| Publication Year: | 2022 |
| Subject Terms: | FOS: Computer and information sciences, Discrete Mathematics (cs.DM), 0206 medical engineering, Populations and Evolution (q-bio.PE), 0102 computer and information sciences, 02 engineering and technology, Fixed-parameter algorithms, 01 natural sciences, Phylogenetic networks, FOS: Biological sciences, FOS: Mathematics, Mathematics - Combinatorics, Combinatorics (math.CO), Hybridization number, Quantitative Biology - Populations and Evolution, 92D15 05C90 05C85 56R10, Computer Science - Discrete Mathematics |
| Description: | We present the first fixed-parameter algorithm for constructing a tree-child phylogenetic network that displays an arbitrary number of binary input trees and has the minimum number of reticulations among all such networks. The algorithm uses the recently introduced framework of cherry picking sequences and runs in $O((8k)^k \mathrm{poly}(n, t))$ time, where $n$ is the number of leaves of every tree, $t$ is the number of trees, and $k$ is the reticulation number of the constructed network. Moreover, we provide an efficient parallel implementation of the algorithm and show that it can deal with up to $100$ input trees on a standard desktop computer, thereby providing a major improvement over previous phylogenetic network construction methods. Code available at https://github.com/nzeh/tree_child_code |
| Document Type: | Article |
| Language: | English |
| ISSN: | 1432-0541 0178-4617 |
| DOI: | 10.1007/s00453-021-00914-8 |
| DOI: | 10.48550/arxiv.1907.08474 |
| Access URL: | http://arxiv.org/pdf/1907.08474 http://arxiv.org/abs/1907.08474 http://resolver.tudelft.nl/uuid:70e72477-d616-4b6f-a275-f16df603453b |
| Rights: | Springer TDM arXiv Non-Exclusive Distribution |
| Accession Number: | edsair.doi.dedup.....5b67a80e5be6fd1c4d01c9c0a5a2c2c6 |
| Database: | OpenAIRE |
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Nájsť tento článok vo Web of Science | Abstract: | We present the first fixed-parameter algorithm for constructing a tree-child phylogenetic network that displays an arbitrary number of binary input trees and has the minimum number of reticulations among all such networks. The algorithm uses the recently introduced framework of cherry picking sequences and runs in $O((8k)^k \mathrm{poly}(n, t))$ time, where $n$ is the number of leaves of every tree, $t$ is the number of trees, and $k$ is the reticulation number of the constructed network. Moreover, we provide an efficient parallel implementation of the algorithm and show that it can deal with up to $100$ input trees on a standard desktop computer, thereby providing a major improvement over previous phylogenetic network construction methods.<br />Code available at https://github.com/nzeh/tree_child_code |
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| ISSN: | 14320541 01784617 |
| DOI: | 10.1007/s00453-021-00914-8 |