Fast Graph Algorithms for Phylogenetics
| Project/Area Number |
26330014
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| Research Category |
Grant-in-Aid for Scientific Research (C)
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| Allocation Type | Multi-year Fund |
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| Section | 一般 |
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| Research Field |
Theory of informatics
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| Research Institution | Kyoto University |
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Principal Investigator |
Jansson Jesper 京都大学, 白眉センター, 特定准教授 (60536100)
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| Project Period (FY) |
2014-04-01 – 2018-03-31
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| Project Status |
Completed (Fiscal Year 2017)
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| Budget Amount *help |
¥4,550,000 (Direct Cost: ¥3,500,000、Indirect Cost: ¥1,050,000)
Fiscal Year 2017: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2016: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
Fiscal Year 2015: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Fiscal Year 2014: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
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| Keywords | Algorithm theory / Computational complexity / Implementations / Graph algorithms / Phylogenetic tree / Consensus tree / Supertree / algorithm / computational complexity / phylogenetic tree / consensus tree |
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| Outline of Final Research Achievements |
We developed fast algorithms for constructing several popular consensus trees: The majority rule consensus tree, the loose consensus tree, the greedy consensus tree, the frequency difference consensus tree, the Adams consensus tree, the R* consensus tree, and two kinds of local consensus trees. Some of them were the first improvements in a long time; for example, the previously fastest algorithm for the Adams consensus tree was from 1972.
Next, we characterized the computational complexity of some fundamental supertree problems and designed approximation algorithms for NP-hard problem variants. We also gave a fast and memory-efficient centroid paths-based algorithm for computing the rooted triplet distance between two phylogenetic trees.
Finally, we presented a fast method for the rooted triplet distance between galled trees (phylogenetic networks whose cycles are disjoint). Our strategy was to transform the galled trees into pairs of trees and apply the fast algorithm for trees.
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Report
(5 results)
Research Products
(36 results)
