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Developing Softwares for Molecular Phylogenetics

Research Project

Project/Area Number 12554037
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section展開研究
Research Field 系統・分類
Research InstitutionThe Institute of Statistical Mathematics

Principal Investigator

HASEGAWA Masami  Institute of Statistical Mathematics, Department of Prediction Theory, Professor, 予測制御研究系, 教授 (60011657)

Co-Investigator(Kenkyū-buntansha) GOTOH Osamu  Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, Project leader, 生命情報, 主任研究員 (40142111)
SHIMODAIRA Hidetoshi  Tokyo Institute of Technology, Lecturer, 情報理工学研究科, 講師 (00290867)
HASHIMOTO Tetsuo  University of Tsukuba, Institute of Biological Sciences, Professor, 生物科学系, 教授 (50208451)
KISHINO Hirohisa  University of Tokyo, Graduate School of Agriculture and Life Sciences, Professor, 農学生命科学研究科, 教授 (00141987)
足立 淳  理化学研究所, ゲノム科学総合研究センター, 研究員
Project Period (FY) 2000 – 2002
Project Status Completed (Fiscal Year 2002)
Budget Amount *help
¥12,900,000 (Direct Cost: ¥12,900,000)
Fiscal Year 2002: ¥3,600,000 (Direct Cost: ¥3,600,000)
Fiscal Year 2001: ¥3,700,000 (Direct Cost: ¥3,700,000)
Fiscal Year 2000: ¥5,600,000 (Direct Cost: ¥5,600,000)
Keywordsmolecular phylogenetics / model misspecification / phylogenetic inference / tree selection / divergence time / molecular clock / adaptive evolution / eutherian mammal / 多重比較 / 分子進化速度 / 階層モデル / 共進化 / 集団サイズ / 遺伝子構造予測 / SINE法 / SINE-flanking配列 / 分子時計 / 進化速度の変動 / 分岐時間推定
Research Abstract

It is prerequisite to establish the phylogenetic relations among organises before studying biological evolution and biodiversity. We developed methods for inferring molecular phylogenies based on the likelihood approach and applied them tb various phylogenetic problems ;
(1) The effect of model misspecification in phylogenetic inference,
(2) Modelling in the phylogenetic inference ofmulti-gene data,
(3) Tests of phylogenetic tree selection,
(4) Methods for estimating divergence times without assuming a molecular clock,
(5) Detecting adaptive molecular evolution,
(6) Phylogenetic evolution of eutherian mammals

Report

(4 results)
  • 2002 Annual Research Report   Final Research Report Summary
  • 2001 Annual Research Report
  • 2000 Annual Research Report
  • Research Products

    (31 results)

All Other

All Publications (31 results)

  • [Publications] T.Pupko, M.Hasegawa et al.: "Combining multiple data sets in a likelihood analysis : which models are best?"Mol. Biol. Evol.. 19. 2294-2307 (2002)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] T.Pupko, M.Hasegawa et al.: "A branch-and-bound algolithm for the inference of ancestral amino-acid sequences when the replacement rate varies among sites : Application to the evolution of five gene families"Bioinformatics. 18. 1116-1123 (2002)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] W.Martin, M.Hasegawa et al.: "Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny of thousands of cyanobacterial genes in the nucleus"Proc. Natl. Acod. Sci. U.S.A.. 99. 12246-12251 (2002)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] Y.Zhong, M.Hasegawa et al.: "Detecting evolutionary rate heterogeneity among mangroves and their close terrestrial relatives"Ecol. Lett.. 5. 427-432 (2002)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] T.-K.Seo, M.Hasegawa, H.Kishino et al.: "Estimation of Effective Population Size of HIV-1 Within a Host: A Pseudomaximum-Likelihood Approach"Genetics. 160. 1283-1293 (2002)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] N.Arisue, T.Hashimoto, M.Hasegawa et al.: "The phylogenetic position of the pelobiont Mastigamoeba balamuti based on sequences of rDNA and translation elongation factors EF-1a and EF-2"J. Euk. Microbiol.. 49. 1-10 (2002)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] H. Shimodaira and M. Hasegawa: "CONSEL : a program for assessing the confidence of phylogenetic tree selection"Bioinformatics. 17. 1246-1247 (2001)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] T.-K Seo, J.L. Thorne, M, Hasegawa, and H. Kishino: "A viral sampling design for testing the molecular clock and for estimating evolutionary rates and divergence times"Bioinformatics. 18. 115-123 (2002)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] T.-K Seo, J.L. Thorne, M. Hasegawa,and H. Kishino: "Estimation of effective population size of HIV-1 within a host : a pseudomaximum-likelihood approach"Genetics. 160. 1283-1293 (2002)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] T. Pupko, I, Pe'er, M. Hasegawa, D.Graur, and N. Friedman: "A branch-and-bound algorithm for the inference of ancestral amino-acid sequences when the replacement rate varies among sites : Application to the evolution of five gene families"Bioinformatics. 18. 1116-1123 (2002)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] T. Pupko, D. Huchon, Y. Cao, N. Okada and M. Hasegawa: "Combining multiple data sets in a likelihood analysis : Which models are the best?"Mol. Biol. Evol.. 19. 2294-2307 (2002)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] H. Shimodaira: ". An approximately unbiased test of phylogenetic tree selection"System. Biol.. 51. 492-508 (2002)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2002 Final Research Report Summary
  • [Publications] T.pupko, M.Hasegawa et al.: "Combining multiple data sets in a likelihood analysis : Which models are best?"Mol. Biol. Evol.,. 19. 2294-2307 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] T.Pupko, M.Hasegawa et al.: "A branch-and-bound algolithm for the inference of ancestral amino-acid sequences when the replacement rete varies among sites : Application to the evolution of five gene families"Bioinformatics. 18. 1116-1123 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] W.Martin, M.Hasegawa et al.: "Evolutionary analysis of Arabidopsis, cyanobacterial and chloraplast genomes reveals plastid phylogeny of thousands of cyanobacterial genomes in the nucleus"Proc. Natl. Acod. Sci : U.S.A.. 99. 12246-12251 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] Y.Zhong, M.Hasegawa et al.: "Detecting evolutionary rate heterogeneity among mangroves and their close terrestrial relatives"Ecol. Lett.. 5. 427-432 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] T.-K.Seo, M.Hasegawa, H.Kishino et al.: "Estimation of effective population size of HIV-1 within a host : a pseudomaximum-likelihood approach"Genetics. 160. 1283-1293 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] N.Arisue, T.Hashimoto, M.Hasegawa et al.: "The phylogenetic position of the pelobiont Mastigamoeba balamuti based on sequences of rDNA and franslation elongation factors EF-1a and EF-2"J. Euk. Microbiol.. 49. 1-10 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] M.Nikaido, F.Matsuno, H.Hamilton, R.L.Brownell Jr., Y.Cao, D.Wang, Z.Zhu, A.M.Shedlock, R.E.Fordyce, M.Hasegawa, N.Okada: "Retroposon analysis of major ceatcean lineages : The monophyly of toothed whales and the paraphyly of river dolpohins"Proceedings of Academy of Scie nce, USA. 98. 7384-7389 (2001)

    • Related Report
      2001 Annual Research Report
  • [Publications] M.Nikaido, K.Kawai, Y.Cao, M.Harada, S.Tomita, N.Okada, M.Hasegawa: "Maximum likelihood analysis of the complete mitochondrial genomes of eutherians and a reevaluation of the phylogeny of bats and insectivores"Journal of Molecular Evolution. 53. 508-516 (2001)

    • Related Report
      2001 Annual Research Report
  • [Publications] H.Shimodaira, M.Hasegawa: "CONSEL : a program for assessing the confidence of phylogenetic tree selection"Bioinformatics. 17. 1246-1247 (2001)

    • Related Report
      2001 Annual Research Report
  • [Publications] T.K.Seo, J.L.Thorne, M.Hasegawa, H.Kishino: "A viral sampling design for testing the molecular clock and for estimating evolutionary rates and divergence times"Bioinformatics. 18. 115-123 (2002)

    • Related Report
      2001 Annual Research Report
  • [Publications] T.-K.Seo, J.L.Thorne, M.Hasegawa, H.Kishino: "Estimation of effective population size of HIV 1 within a host : A pseudo-maximum likelihood approach"Genetics. (印刷中). (2002)

    • Related Report
      2001 Annual Research Report
  • [Publications] J.L.Thorne, H.Kshino: "Divergence time and evolutionary rate estimation with multilocus data"Systematic Biology. (印刷中). (2002)

    • Related Report
      2001 Annual Research Report
  • [Publications] H.Shimodaira: "Approximately unbiased test of phylogenetic tree selection"Systematic Biology. (印刷中). (2002)

    • Related Report
      2001 Annual Research Report
  • [Publications] 後藤修: "配列のホモロジーと統計情報を併用した真核生物遺伝子構造の予測"統計数理. (印刷中). (2002)

    • Related Report
      2001 Annual Research Report
  • [Publications] Ota,R. et al: "Appropriate likelihood ratio test and marginal distributions for evolutionary tree models with constrains on parameters"Molecular Biology and Evolution. 17(5). 798-803 (2000)

    • Related Report
      2000 Annual Research Report
  • [Publications] Lum,J.K. et al.: "Consistency of SINE insertion topology and flanking sequence tree : Quantifying relationship among cetartiodactyls"Molecular Biology and Evolution. 17(10). 1417-1424 (2000)

    • Related Report
      2000 Annual Research Report
  • [Publications] Cao,Y. et al.: "Phylogenetic position of turtles among amniotes : evidence from mitochondrial and nuclear genes"Gene. 259. 139-148 (2000)

    • Related Report
      2000 Annual Research Report
  • [Publications] Cao,Y. et al.: "Interordinal relationship and timescale of enthrian evolution as inferred from mitochondrial genome date"Gene. 259. 149-158 (2000)

    • Related Report
      2000 Annual Research Report
  • [Publications] Kishino,H. et al.: "Performance of a divergence time estimation method under a probabilistic model of rate evolution"Molecular Biology and Evolution. 18(3). 352-361 (2001)

    • Related Report
      2000 Annual Research Report

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Published: 2000-04-01   Modified: 2016-04-21  

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