2016 Fiscal Year Research-status Report
Fast Graph Algorithms for Phylogenetics
| Project/Area Number |
26330014
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| Research Institution | Kyoto University |
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Principal Investigator |
ジャンソン ジェスパー 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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| Keywords | algorithm / computational complexity / phylogenetic tree / consensus tree |
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| Outline of Annual Research Achievements |
We developed new algorithms that are faster than all the previously known ones for a number of popular types of consensus trees (majority rule consensus tree, loose consensus tree, greedy consensus tree, R* consensus tree, etc.). We also proved that two variants of the local consensus tree problem in which the goal is to construct a minimal phylogenetic tree (where "minimal" means either having the smallest possible number of internal nodes or the smallest possible number of resolved triplets) that contains every resolved triplet present in all of the input trees trees are NP-hard and gave exact, exponential-time solutions for both problems. The second variant generalizes the RV-II tree, introduced by Kannan, Warnow, and Yooseph in 1998. Furthermore, for the rooted triplet consistency problem, we characterized how the computational complexity changes under various restrictions and obtained a linear-time algorithm for dense inputs with no forbidden resolved triplets.
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| Current Status of Research Progress |
Current Status of Research Progress
2: Research has progressed on the whole more than it was originally planned.
Reason
In FY2016, we published several peer-reviewed conference papers and journal articles related to the topics in the grant application. In particular, our main results on consensus trees appeared in Journal of the ACM, one of the top journals in our field. We are currently working on fast algorithms for computing the rooted triplet distance between two phylogenetic networks; for the special case where all cycles in the underlying undirected graphs are disjoint, we have recently discovered a method that can do it in subquadratic time by transforming the input so that the answer can be obtained by applying an existing algorithm for the simpler case of two phylogenetic trees a constant number of times.
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| Strategy for Future Research Activity |
As planned.
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| Causes of Carryover |
The flight to Copenhagen was cheaper than expected.
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| Expenditure Plan for Carryover Budget |
To buy some equipment for backups.
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