Comparing and Combining Trees

• Project/Area Number: 23700011
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Multi-year Fund
• Research Field: Fundamental theory of informatics
• Research Institution: Kyoto University (2012-2013); Ochanomizu University (2011)
• Principal Investigator: JANSSON Jesper 京都大学, 白眉センター, 特定准教授 (60536100)
• Project Period (FY): 2011 – 2013
• Project Status: Completed (Fiscal Year 2013)
• Budget Amount: ¥3,380,000 (Direct Cost: ¥2,600,000、Indirect Cost: ¥780,000); Fiscal Year 2013: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000); Fiscal Year 2012: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000); Fiscal Year 2011: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
• Keywords: アルゴリズム / 計算複雑さ / 系統樹 / algorithm / computational complexity / phylogenetic tree / consensus tree / rooted triplet distance / 計算複雑性 / 順序木 / 超系統樹 / 合意樹 / 類似度

Research Abstract

The purpose of this research project was to develop efficient algorithms for comparing and combining trees involving huge datasets. It focused on three particular topics: (i) Building a minimally resolved supertree; (ii) Constructing a consensus tree; and (iii) Measuring the similarity of two treelike structures.
Some new theoretical algorithms were designed and analyzed, and a number of related computational complexity results were obtained.

Research Products

• [Journal Article] Computing the Rooted Triplet Distance between Galled Trees by Counting Triangles (2014)
  • Author(s): J. Jansson and A. Lingas
  • Journal Title: Journal of Discrete Algorithms Volume: Vol.25 Pages: 66-78
  • DOI: 10.1016/j.jda.2013.10.002
• [Journal Article] Constructing the R* Consensus Tree of Two Trees in Subcubic Time (2013)
  • Author(s): J. Jansson and W.-K. Sung
  • Journal Title: Algorithmica Volume: Vol.66, Number2 Issue: 2 Pages: 329-345
  • DOI: 10.1007/s00453-012-9639-1
• [Journal Article] An Optimal Algorithm for Building the Majority Rule Consensus Tree (2013)
  • Author(s): J. Jansson, C. Shen, and W.-K. Sung
  • Journal Title: Lecture Notes in Computer Science (RECOMB 2013) Volume: 7821 Pages: 88-99
  • Peer Reviewed
• [Journal Article] Algorithms for the Majority Rule (+) Consensus Tree and the Frequency Difference Consensus Tree (2013)
  • Author(s): J. Jansson, C. Shen, and W.-K. Sung
  • Journal Title: Lecture Notes in Computer Science (WABI 2013) Volume: 8126 Pages: 141-155
  • Peer Reviewed
• [Journal Article] Improved Algorithms for Constructing Consensus Trees. (2013)
  • Author(s): J. Jansson, C. Shen, and W.-K. Sung.
  • Journal Title: Proc. of SODA 2013 Volume: 2013 Pages: 1800-1813
  • Peer Reviewed
• [Journal Article] Faster Computation of the Robinson-Foulds Distance between Phylogenetic Networks (2012)
  • Author(s): Tetsuo Asano, Jesper Jansson, Kunihiko Sadakane, Ryuhei Uehara, Gabriel Valiente
  • Journal Title: Information Sciences Volume: 197 Pages: 77-90
  • DOI: 10.1016/j.ins.2012.01.038
  • NAID: 120003184350
  • Peer Reviewed
• [Journal Article] Polynomial-Time Algorithms for Building a Consensus MUL-Tree (2012)
  • Author(s): Y. Cui, J. Jansson, and W.-K. Sung
  • Journal Title: Journal of Computational Biology Volume: Vol.19, Number9 Issue: 9 Pages: 1073-1088
  • DOI: 10.1089/cmb.2012.0008
• [Journal Article] Ultra-succinct representation of ordered trees with applications (2012)
  • Author(s): Jesper Jansson, Kunihiko Sadakane, Wing-Kin Sung
  • Journal Title: Journal of Computer and System Sciences Volume: 78(2) Issue: 2 Pages: 619-631
  • DOI: 10.1016/j.jcss.2011.09.002
  • Peer Reviewed
• [Journal Article] The Complexity of Inferring a Minimally Resolved Phylogenetic Supertree (2012)
  • Author(s): J. Jansson, R. S. Lemence, and A. Lingas
  • Journal Title: SIAM Journal on Computing Volume: Vol.41, Number1 Issue: 1 Pages: 272-291
  • DOI: 10.1137/100811489
• [Journal Article] Faster computation of the Robinson-Foulds distance between phylogenetic networks. (2012)
  • Author(s): T. Asano, J. Jansson, K. Sadakane, R. Uehara, and G. Valiente.
  • Journal Title: Information Sciences Volume: 197 Pages: 77-90
  • Peer Reviewed
• [Journal Article] Polynomial-Time Algorithms for Building a Consensus MUL-Tree. (2012)
  • Author(s): Y. Cui, J. Jansson, and W.-K. Sung.
  • Journal Title: Journal of Computational Biology Volume: 19 Pages: 1073-1088
  • Peer Reviewed
• [Journal Article] Computing the Rooted Triplet Distance between Galled Trees by Counting Triangles. (2012)
  • Author(s): J. Jansson and A. Lingas.
  • Journal Title: Lecture Notes in Computer Science Volume: 7354 Pages: 385-398
  • Peer Reviewed
• [Journal Article] Upper and Lower Degree Bounded Graph Orientation with Minimum Penalty (2012)
  • Author(s): Y. Asahiro, J. Jansson, E. Miyano, H. Ono
  • Journal Title: Australian Computer Science Communications Volume: 34
  • Peer Reviewed
• [Journal Article] Algorithms for Building Consensus MUL-trees (2011)
  • Author(s): Y. Cui, J. Jansson, W.-K. Sung
  • Journal Title: Lecture Notes in Computer Science Volume: 7074 Pages: 744-753
  • DOI: 10.1007/978-3-642-25591-5_76
  • ISBN: 9783642255908, 9783642255915
  • Peer Reviewed
• [Presentation] Algorithms for the Majority Rule (+) Consensus Tree and the Frequency Difference Consensus Tree (2013)
  • Author(s): J. Jansson, C. Shen, and W.-K. Sung
  • Organizer: Proceedings of the Thirteenth International Workshop on Algorithms in Bioinformatics (WABI 2013), Lecture Notes in Computer Science
  • Place of Presentation: Nice, France(Vol.8126, pp.141-155, Springer-Verlag, 2013)
• [Presentation] An Optimal Algorithm for Building the Majority Rule Consensus Tree (2013)
  • Author(s): J. Jansson, C. Shen, and W.-K. Sung
  • Organizer: Proceedings of the Seventeenth Annual International Conference on Research in Computational Molecular Biology (RECOMB 2013), Lecture Notes in Computer Science
  • Place of Presentation: Beijing, China(Vol. 7821, pp. 88-99, Springer-Verlag, 2013)
• [Presentation] Improved Algorithms for Constructing Consensus Trees (2013)
  • Author(s): J. Jansson, C. Shen, and W.-K. Sung
  • Organizer: Proceedings of the Twenty-Fourth Annual ACM-SIAM Symposium on Discrete Algorithms (SODA 2013), Society for Industrial and Applied Mathematics (SIAM), 2013
  • Place of Presentation: New Orleans, U.S.A.(pp. 1800-1813)
• [Presentation] Computing the Rooted Triplet Distance between Galled Trees by Counting Triangles (2012)
  • Author(s): J. Jansson and A. Lingas
  • Organizer: Proceedings of the Twenty-Third Annual Symposium on Combinatorial Pattern Matching (CPM 2012), Lecture Notes in Computer Science
  • Place of Presentation: Helsinki, Finland(Vol. 7354, pp. 385-398,Springer-Verlag, 2012)
• [Presentation] Upper and Lower Degree Bounde d Graph Orientation with Minimum Penalty (2012)
  • Author(s): Y. Asahiro, J. Jansson, E. Miyano, and H. Ono
  • Organizer: Proceedings of Computing : the Eighteenth Australasian Theory Symposium (CATS 2012), Australian Computer Science Communications
  • Place of Presentation: Melbourne, Australia(Vol.34, Number 8, pp. 139-146, Australian Computer Society Inc., 2012)
• [Presentation] Algorithms for Building Consensus MUL-trees (2011)
  • Author(s): Y. Cui, J. Jansson, and W.-K. Sung
  • Organizer: Proceedings of the Twenty-Second International Symposium on Algorithms and Computation (ISAAC 2011), Lecture Notes in Computer Science
  • Place of Presentation: Yokohama, Japan(Vol. 7074, pp. 744-753, Springer-Verlag, 2011)
  • Year and Date: 2011-12-05
• [Presentation] Algorithms for Building Consensus MUL-trees (2011)
  • Author(s): Jesper Jansson
  • Organizer: The Twenty-Second International Symposium on Algorithms and Computation (ISAAC 2011)
  • Place of Presentation: 横浜
• [Presentation] Algorithms for the Majority Rule (+) Consensus Tree and the Frequency Difference Consensus Tree
  • Author(s): J. Jansson
  • Organizer: Thirteenth International Workshop on Algorithms in Bioinformatics (WABI 2013)
  • Place of Presentation: Nice, France
• [Remarks]
  • URL: http://sunflower.kuicr.kyoto-u.ac.jp/~jj/
• [Remarks] Jesper Jansson's webpage
  • URL: http://sunflower.kuicr.kyoto-u.ac.jp/~jj/
• [Remarks] FACT: Fast Algorithms for Consensus Trees
  • URL: http://compbio.ddns.comp.nus.edu.sg/~consensus.tree/
• [Remarks] Jesper Jansson's webpage
  • URL: http://sunflower.kuicr.kyoto-u.ac.jp/~jj/
• [Remarks] FACT: Fast Algorithms for Consensus Trees
  • URL: http://compbio.ddns.comp.nus.edu.sg/~consensus.tree/
• [Remarks]
  • URL: http://www.cf.ocha.ac.jp/acpro/jj/