• Search Research Projects
  • Search Researchers
  • How to Use
  1. Back to previous page

Development of software for analyzing gene sequence data

Research Project

Project/Area Number 05558024
Research Category

Grant-in-Aid for Developmental Scientific Research (B)

Allocation TypeSingle-year Grants
Research Field Statistical science
Research InstitutionThe Institute of Statistical Mathematics

Principal Investigator

HASEGAWA Masami  The Inst.of Statist.Math., Prof., 予測制御研究系, 教授 (60011657)

Co-Investigator(Kenkyū-buntansha) YANO Taka-aki  Showa Univ., Assoc.Prof., 教養部, 助教授 (70081792)
KISHINO Hirohisa  Univ.Tokyo, Assoc.Prof., 教養学部, 助教授 (00141987)
HASHIMOTO Tetsuo  The Inst.of Statist.Math., Assoc.Prof., 教育情報センター, 助教授 (50208451)
安永 照雄  大阪大学, 遺伝情報実験施設, 助教授
Project Period (FY) 1993 – 1995
Project Status Completed (Fiscal Year 1995)
Budget Amount *help
¥12,900,000 (Direct Cost: ¥12,900,000)
Fiscal Year 1995: ¥1,200,000 (Direct Cost: ¥1,200,000)
Fiscal Year 1994: ¥3,000,000 (Direct Cost: ¥3,000,000)
Fiscal Year 1993: ¥8,700,000 (Direct Cost: ¥8,700,000)
Keywordsevolutionary tree / maximum likelihood / Markov model / mitochondrial DNA / amino acid substitution / transition matrix / approximate likelihood / local rearrangement / RNA / 蛋白質 / 確率モデル / タンパク質 / アミノ酸置換 / モデル / シミュレーション / MOLPHY
Research Abstract

We have developed maximum likelihood (ML) methods for inferring evolutionary trees from DNA and protein sequences. Since it is important to use realistic models for the substitution process in the ML analyzes, we have developed several models for the nucleotide and amino acid substitutions. Among them, a Markov model for amino acid substitution of mitochondrial DNA-encoded proteins might be the most important. In recent years, mitochondrial DNA sequences have been used widely in molecular phylogenetics. However, since the genetic code of mitochondria differs a little from the universal code, and since most of the mitochondrial proteins are membraneous, the transition matrix specific to the mtDNA-encoded proteins might be different from those of the models which are mainly based on the proteins encoded by nuclear DNA.Therefore, we estimated the matrix for the mtDNA-encoded proteins from 22 completely sequenced data of vertebrates by the ML.This matrix would be useful in analyzing mtDNA-encoded proteins.
Since the ML method is computationally intensive, mainly due to a huge number of possible trees, there exists several limitations in applying the method to real biological problems. We have developed several methods to reduce the computational burden of the ML analyzes ; i.e., (1) approximate likelihood method to reduce the number of candidate trees, (2) star-decomposition method for topology search, (3) local rearrangement method for topology search.
These results have been implemented in our program package MOLPHY,which are available from the network and have already been used widely in the world.

Report

(4 results)
  • 1995 Annual Research Report   Final Research Report Summary
  • 1994 Annual Research Report
  • 1993 Annual Research Report
  • Research Products

    (55 results)

All Other

All Publications (55 results)

  • [Publications] M. Hasegawa and H. Kishino,: "Accuracies of the simple methods for estimating the bootstrap probability of a maximum likehood tree" Mol. Biol. Evol.11. 142-145 (1994)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] Y. Cao et al.,: "Phylogenetic relationships among eutherian orders estimated from inferred sequences of mitochondrial proteins." J. Mol. Evol.39. 519-527 (1994)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] J.Adachi and M. Hasegawa.: "Improved dating of the human-chimpanzee separation in the mitochondrial DNA tree : heterogeneity among amino acid sites." J. Mol. Evol.40. 622-628 (1995)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] J.Adachi and M. Hasegawa.: "Phylogeny of whales : dependence of the inference on species sampling." Mol. Biol. Evol.12. 177-179 (1995)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] J.Adachi and M. Hasegawa.: "Tempo and mode of synonymous substitutions in mitochondrial DNA of primates." Mol. Biol. Evol.13. 200-208 (1996)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] J.Adachi and M. Hasegawa.: "Model of amino acid substitution in proteins encoded by mitochondrial DNA." J. Mol. Evol.(in press). (1996)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] 長谷川政美,岸野洋久: "分子系統学" 岩波書店, 257 (1996)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] T.Hashimoto et al.: "Protein phylogeny gives a robust estimation for early divergences of eukaryotes : phylogenetic place of a mitochondria-lacking protozoan, Giardia lamblia" Mol.Biol.Evol.11. 65-71 (1994)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] M.Hasegawa and H.Kishino: "Accuracies of the simple methods for estimating the bootstrap probability of a maximum likehood tree" Mol.Biol.Evol.11. 142-145 (1994)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] Y.Cao et al.: "Phylogenetic place of guinea pigs : no support of the rodent polyphyly hypothesis from maximum likehood analyzes of multiple protein sequences" Mol.Biol.Evol.11. 593-604 (1994)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] S.Yokobori et al.: "Relationship among coelacanths, lungfishes and tetrapods ; a phylogenetic analysis besed on mitochondrial cytochrome oxidase I gene sequences" J.Mol.Evol.38. 602-609 (1994)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] Y.Cao et al.: "Phylogenetic relationships among eutherian orders estimated from inferred sequences of mitochondrial proteins" J.Mol.Evol.39. 519-527 (1994)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] T.Shirakura et al.: "Phylogenetic place of a mitochondria-lacking protozoan, Entamoeba histolytica, inferred from amino acid sequences of elongation factor 2" Jpn.J.Genet.69. 119-135 (1994)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] Y.Cao et al.: "Eutherian phylogeny as inferred from mitochondrial DNA sequence data" Jpn.J.Genet.69. 455-472 (1994)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] J.Adachi and M.Hasegawa: "Improved dating of the human-chimpanzee separation in the mitochondrial DNA tree : heterogeneity among amino acid sites" J.Mol.Evol.40. 622-628 (1995)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] S.Chow and H.Kishino: "Phylogenetic relationships between tuna species of the genus Thunnus (Scombridae : Teleostei) : Inconsistent implications from morphology, nuclear and mitochondrial genomes" J.Mol.Evol.41. 741-748 (1995)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] J.Adachi and M.Hasegawa: "Phylogeny of whales : dependence of the inference on species sampling" Mol.Biol.Evol.12. 177-179 (1995)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] T.Hashimoto et al.: "Phylogenetic place of a mitochondrion-lacking protozoan, Giardia lamblia, inferred from amino acid sequences of elongation factor 2" Mol.Biol.Evol.12. 782-793 (1995)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] T.Hashimoto et al.: "Phylogenetic place of kinetoplastid protozoa inferred from protein phylogeny of elongation factor 1alpha" Mol.Biochem.Parasitol.70. 181-185 (1995)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] K.Mizuta et al.: "The evolutionary relationships between homologs of ribosomal YL8 protein and YL8-like protein" Curr.Genet.28. 19-25 (1995)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] A.Yamamoto et al.: "Nucleotide sequence of the SrRNA gene of Entamoeba gingivalis : applications for construction of a species-specific DNA probe and phylogenetic analysis" Microbiol.Immunol.39. 185-192 (1995)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] J.Adachi and M.Hasegawa: "Tempo amd mode of synonymous substitutions in mitochondrial DNA of primates" Mol.Biol.Evol.13. 200-208 (1996)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] Y.Nakamura et al.: "Phylogenetic place of kinetoplastid protozoa inferred from protein phylogenies of elongation factors 1alpha and 2" J.Biochem.119. 70-79 (1996)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] T.Hashimoto and M.Hasegawa: "Origin and early evolution of eukaryotes inferred from the amino acid sequences of translation elongation factors 1alpha/Tu and 2/G" Adv.Biophys.32. 73-120 (1996)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] T.Kamaishi et al.: "Protein phylogeny of EF-1alpha suggests microsporidians are extremely ancient eukaryotes" J.Mol.Evol.(in press).

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] J.Adachi and M.Hasegawa: "Instability of quarted analyzes of molecular sequence data by the maximum likelihood method : The Cetacea/Artiodactyla relationships" Mol.Phyl.Evol.(in Press).

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] J.Adachi and M.Hasegawa: "Model of amino acid substitution in proteins encoded by mitochondrial DNA" J.Mol.Evol.(in Press).

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] M.Hasegawa and J.Adachi: "Phylogenetic position of cetaceans relative to artiodactyls : Reanalysis of mitochondrial and nuclear sequences" Mol.Biol.Evol.(in press).

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] Y.Nakamura et al.: "Phylogenetic position of Blastocystis hominis that contains cytochrome-free mitochondria, inferred from the protein phylogeny of elongation factor 1alpha" Mol.Biochem.Parasit.(in press).

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1995 Final Research Report Summary
  • [Publications] Hashimoto,T.et al.: "Phylogenetic place of a mitochondrion-lacking protozoan,Giardia lamblia,inferred from amino acid sequences of elongation factd 2." Mol.Biol.Evol.12. 782-793 (1995)

    • Related Report
      1995 Annual Research Report
  • [Publications] Hashimoto,T.et al.: "Phylogenetic place of kinetoplastid protozoa inferred from a protein phylogeny of elongation factor 1α." Mol.Biochem.Parasitol.70. 181-185 (1995)

    • Related Report
      1995 Annual Research Report
  • [Publications] Adachi,J.,Hasegawa,M.: "Phylogeny of whales : dependence of the inference on species sampling." Mol.Biol.Evol.12. 177-179 (1995)

    • Related Report
      1995 Annual Research Report
  • [Publications] Adachi,J.,Hasegawa,M.: "Improved dating of the human-chimpanzee separation in the mitochondrial DNA tree : heterogeneity among amino acid sites." J.Mol.Evol.40. 622-628 (1995)

    • Related Report
      1995 Annual Research Report
  • [Publications] Adachi,J.,Hasegawa,M.: "Tempo and mode of synonymous substitutions in mitochondrial DNA of primates." Mol.Biol.Evol.13. 200-208 (1996)

    • Related Report
      1995 Annual Research Report
  • [Publications] Nakamura.Y,et al.: "Phylogenetic place of kinetoplastid protozoa inferred from protein phylogenies of elongation factors 1α and 2." J.Biochem.119. 70-79 (1996)

    • Related Report
      1995 Annual Research Report
  • [Publications] Hashimoto,T.,Hasegawa,M.: "Origin and early evolution of eukaryotes inferred from the amino acid sequences of translation elongation factors 1α/Tu and 2/G" Advances in Biophysics. 32. 73-120 (1996)

    • Related Report
      1995 Annual Research Report
  • [Publications] Adachi,J.,Hasegawa,M.: "Model of amino acid substitution in proteins encoded by mitochondrial DNA." J.Mol.Evol.(in press). (1996)

    • Related Report
      1995 Annual Research Report
  • [Publications] Adachi,J.,Hasegawa,M.: "Instability of quartet analyses of molecular sequence data by the maximum likelihood method : The Cetaceal Artiodactyla relationships." Mol.Phyl.Evol.(in press). (1996)

    • Related Report
      1995 Annual Research Report
  • [Publications] Hasegawa,M.,Adachi,J.: "Phylogenetic position of cetaceans relative to artiodactyls : Reanalysis of mitochondrial and nuclear sequences." Mol.Biol.Evol.(in press). (1996)

    • Related Report
      1995 Annual Research Report
  • [Publications] Chow,S.,Kishino,H.: "Phylogenetic relationships between tuna species of the genus Thunnus" J.Mol.Evol.41. 741-748 (1995)

    • Related Report
      1995 Annual Research Report
  • [Publications] 松石隆,岸野洋久,沼知健一: "種苗放流による遺伝子のおきかわりに関する数理モデル" 日本水産学会誌. 61. 326-330 (1995)

    • Related Report
      1995 Annual Research Report
  • [Publications] Adachi,J.,Hasegawa,M.: "The Origin and Past of Modern Humans as Viewod from DNA (S.Brenner and K.Hanihara,eds.)" World Scientific Publ., 23 (1995)

    • Related Report
      1995 Annual Research Report
  • [Publications] 長谷川政美、岸野洋久: "分子系統学" 岩波書店(印刷中), 250 (1996)

    • Related Report
      1995 Annual Research Report
  • [Publications] Hashimoto,T.: "Protein phylogeny jwes a robust estimation for early divergences" Molecular Biology and Evolution. 11. 65-71 (1994)

    • Related Report
      1994 Annual Research Report
  • [Publications] Hasegawa,M.: "Accuracies of the simple methods for estimeting the bootstrap probability" Molecular Biology and Evolution. 11. 142-145 (1994)

    • Related Report
      1994 Annual Research Report
  • [Publications] Cao,Y.: "Phylogenetic place of guinea‐pigs" Molecular Biology and Evolution. 11. 593-604 (1994)

    • Related Report
      1994 Annual Research Report
  • [Publications] Yokobori,S.: "Relationship among coelacanths,lungfishes and tetrapods" Journal of Molecular Evolution. 38. 602-609 (1994)

    • Related Report
      1994 Annual Research Report
  • [Publications] Cao,Y.: "Phylogenetic relationships among eutherian orders" Journal of Molecular Evolution. 39. 519-527 (1994)

    • Related Report
      1994 Annual Research Report
  • [Publications] Adachi,J.: "Phylogeng of whales" Molecular Biology and Evolution. 12. 177-179 (1995)

    • Related Report
      1994 Annual Research Report
  • [Publications] M.Hasegawa,T.Hashimoto: "Ribosomal RNA trees misleading?" Nature. 361. 23-23 (1993)

    • Related Report
      1993 Annual Research Report
  • [Publications] J.Adachi,Y.Cao,M.Hasegawa: "Tempo and mode of mitochondrid DNA evolution" Journal of Molecular Evolution. 36. 270-281 (1993)

    • Related Report
      1993 Annual Research Report
  • [Publications] M.Hasegawa et al.: "Early branchings in the evolution of eukaryotes" Journal of Molecular Evolution. 36. 380-388 (1993)

    • Related Report
      1993 Annual Research Report
  • [Publications] M.Hasegawa et al.: "Toward a more accurate time scale for the human mt DNA tree" Journal of Molecular Evolution. 37. 347-354 (1993)

    • Related Report
      1993 Annual Research Report
  • [Publications] M.Hasegawa,M.Fujiwara: "Relative efficiencies of ML,MP and NJ methods" Molecular Phylogenetics and evolution. 2. 1-5 (1993)

    • Related Report
      1993 Annual Research Report
  • [Publications] M.Hasegawa,H.Kishino: "Accuracies of the simple methods for estimating the bootstrap probability" Molecular Biology and Evolution. 11. 142-145 (1994)

    • Related Report
      1993 Annual Research Report

URL: 

Published: 1993-04-01   Modified: 2016-04-21  

Information User Guide FAQ News Terms of Use Attribution of KAKENHI

Powered by NII kakenhi