2014 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 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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| 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, 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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| Strategy for Future Research Activity |
As planned.
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| Causes of Carryover |
I would like to use this money to attend a workshop on Phylogenetic Networks in July, 2015.
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| Expenditure Plan for Carryover Budget |
To attend a workshop on Phylogenetic Networks in July, 2015.
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