2015 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, 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 obtained several new results on the approximability of a generalization of the maximum rooted triplets consistency problem in which the input contains a set of 'required' rooted triplets and a set of 'forbidden' rooted triplets, and the objective is to construct a phylogenetic tree that is consistent with as much of the input as possible. We also developed a fast and memory-efficient algorithm for computing the rooted triplet distance between two phylogenetic trees with identical leaf label sets, using the recent framework by Brodal et al. [SODA 2013] but replacing the hierarchical decomposition tree by a simpler centroid paths-based data structure.
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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
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, FY2015 would focus on topics (B) and (C).
In FY2015, we obtained some new results for topic (B) that were presented at the CPM 2015 and AlCoB 2015 conferences. See point 9. above for a description of the results related to topic (B) and point 13. below for the publication details. I also attended a one-week workshop on phylogenetic networks in Singapore in July 2015 to learn more about the state-of-the-art research in this field and to find new, challenging problems for topic (C).
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| Strategy for Future Research Activity |
As planned.
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