研究課題/領域番号 |
26330014
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研究機関 | 京都大学 |
研究代表者 |
ジャンソン ジェスパー 京都大学, 白眉センター, 准教授 (60536100)
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研究期間 (年度) |
2014-04-01 – 2018-03-31
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キーワード | algorithm / computational complexity / phylogenetic tree / consensus tree |
研究実績の概要 |
We improved the running times of the fastest known algorithms for computing two different types of consensus trees, namely the R* consensus tree and the Adams consensus tree. Given a set of k conflicting rooted phylogenetic trees with n leaves each and identical leaf label sets, our new algorithms for the R* consensus tree run in O(n**2) time for k=2, O(n**2 log**(4/3) n) time for k=3, and O(n**2 log**(k+2) n) time for unbounded k. Our algorithms for the Adams consensus tree run in O(n log n / (log log n)) time for k=2 and O(k n log n) time for unbounded k, for the first time beating the widely used O(k n**2)-time algorithm invented by Adams in 1972. To obtain our results, we extended a wavelet tree-based technique for orthogonal range counting on a grid by Bose et al. [WADS 2009].
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現在までの達成度 (区分) |
現在までの達成度 (区分)
2: おおむね順調に進展している
理由
My grant application proposed three related research topics: (A) Constructing different types of consensus trees; (B) Identifying common sub- and superstructures of a set of phylogenetic trees; (C) The combinatorics of phylogenetic networks. According to the grant application, FY2014 would focus on topics (A) and (B).
In FY2014, we obtained some new results for topic (A) that were presented at the ISAAC 2014 and STACS 2015 conferences. See point 9. above for a description of the results related to topic (A) and point 13. below for the publication details. We also obtained some preliminary results for topic (B) regarding the polynomial-time approximability of the NP-hard problem of constructing a phylogenetic supertree consistent with as many of the triplets as possible in an input set of fan triplets and resolved triplets, which will be published in FY2015.
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今後の研究の推進方策 |
As planned.
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次年度使用額が生じた理由 |
I would like to use this money to attend a workshop on Phylogenetic Networks in July, 2015.
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次年度使用額の使用計画 |
To attend a workshop on Phylogenetic Networks in July, 2015.
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