메뉴 건너뛰기




Volumn 31, Issue 4, 2014, Pages 1029-1039

Tests for two trees using likelihood methods

Author keywords

KH test; Maximum likelihood; SOWH test; Topology test

Indexed keywords

ALTERNATIVE HYPOTHESIS; ARTICLE; BOOTSTRAPPING; KISHINO HASEGAWA TEST STATISTIC; LIKELIHOOD RATIO; LIKELIHOOD RATIO TEST; NORMAL DISTRIBUTION; NULL HYPOTHESIS; PERFORMANCE; PROBABILITY; SIMULATION; STATISTICAL MODEL; THEORY;

EID: 84897824687     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msu039     Document Type: Article
Times cited : (15)

References (30)
  • 1
    • 0029974748 scopus 로고    scopus 로고
    • Model of amino acid substitution in proteins encoded by mitochondrial DNA
    • Adachi J, Hasegawa M. 1996. Model of amino acid substitution in proteins encoded by mitochondrial DNA. J Mol Evol. 42:459-468.
    • (1996) J Mol Evol. , vol.42 , pp. 459-468
    • Adachi, J.1    Hasegawa, M.2
  • 2
    • 44649144588 scopus 로고    scopus 로고
    • Identifiability of a Markovian model of molecular evolution with gamma-distributed rates
    • Allman ES, Ané C, Rhodes JA. 2008. Identifiability of a Markovian model of molecular evolution with gamma-distributed rates. Adv Appl Prob. 40:229-249.
    • (2008) Adv Appl Prob. , vol.40 , pp. 229-249
    • Allman, E.S.1    Ané, C.2    Rhodes, J.A.3
  • 3
    • 84868010795 scopus 로고    scopus 로고
    • When do phylogenetic mixture models mimic other phylogenetic models
    • Allman ES, Rhodes JA, Sullivant S. 2012. When do phylogenetic mixture models mimic other phylogenetic models. Syst Biol. 61: 1049-1059.
    • (2012) Syst Biol. , vol.61 , pp. 1049-1059
    • Allman, E.S.1    Rhodes, J.A.2    Sullivant, S.3
  • 4
    • 33745256005 scopus 로고    scopus 로고
    • Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative
    • Anisimova M, Gascuel O. 2006. Approximate likelihood-ratio test for branches: a fast, accurate, and powerful alternative. Syst Biol. 55: 539-552.
    • (2006) Syst Biol. , vol.55 , pp. 539-552
    • Anisimova, M.1    Gascuel, O.2
  • 6
    • 0000485156 scopus 로고
    • Some asymptotic theory for the bootstrap
    • Bickel PJ, Freedman DA. 1981. Some asymptotic theory for the bootstrap. Ann Stat. 9:1196-1217.
    • (1981) Ann Stat. , vol.9 , pp. 1196-1217
    • Bickel, P.J.1    Freedman, D.A.2
  • 8
    • 0030588055 scopus 로고    scopus 로고
    • Full reconstruction of Markov models on evolutionary trees: Identifiability and consistency
    • Chang JT. 1996. Full reconstruction of Markov models on evolutionary trees: identifiability and consistency. Math Biosci. 137: 51-73.
    • (1996) Math Biosci. , vol.137 , pp. 51-73
    • Chang, J.T.1
  • 9
    • 27844438226 scopus 로고    scopus 로고
    • Genome-scale evidence of the nematodearthropod clade
    • Dopazo H, Dopazo J. 2005. Genome-scale evidence of the nematodearthropod clade. Genome Biol. 6:R41.
    • (2005) Genome Biol. , vol.6
    • Dopazo, H.1    Dopazo, J.2
  • 10
    • 0003242435 scopus 로고
    • The jacknife, the bootstrap and other resampling plans
    • Philadelphia (PA): Society for Industrial and Applied Mathematics
    • Efron B. 1982. The jacknife, the bootstrap and other resampling plans. CBMS-NF regional conference series in applied mathematics, Vol. 38. Philadelphia (PA): Society for Industrial and Applied Mathematics.
    • (1982) CBMS-NF Regional Conference Series in Applied Mathematics , vol.38
    • Efron, B.1
  • 11
    • 0034351387 scopus 로고    scopus 로고
    • Likelihood-based tests of topologies in phylogenetics
    • Goldman N, Anderson JP, Rodrigo AG. 2000. Likelihood-based tests of topologies in phylogenetics. Syst Biol. 49:652-670.
    • (2000) Syst Biol. , vol.49 , pp. 652-670
    • Goldman, N.1    Anderson, J.P.2    Rodrigo, A.G.3
  • 12
    • 0000207265 scopus 로고
    • Confidence limits on the maximumlikelihood estimate of the hominoid tree from mitochondrial- DNA sequences
    • Hasegawa M, Kishino H. 1989. Confidence limits on the maximumlikelihood estimate of the hominoid tree from mitochondrial- DNA sequences. Evolution 43:672-677.
    • (1989) Evolution , vol.43 , pp. 672-677
    • Hasegawa, M.1    Kishino, H.2
  • 13
    • 0022376704 scopus 로고
    • Dating the human-ape splitting by a molecular clock of mitochondrial DNA
    • Hasegawa M, Kishino H, Yano T. 1985. Dating the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol. 22: 160-174.
    • (1985) J Mol Evol. , vol.22 , pp. 160-174
    • Hasegawa, M.1    Kishino, H.2    Yano, T.3
  • 14
    • 0024307824 scopus 로고
    • Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea
    • Kishino H, Hasegawa M. 1989. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea. J Mol Evol. 29: 170-179.
    • (1989) J Mol Evol. , vol.29 , pp. 170-179
    • Kishino, H.1    Hasegawa, M.2
  • 15
    • 0025181359 scopus 로고
    • Maximum likelihood inference of protein phylogeny and the origin of chloroplasts
    • Kishino H, Miyata T, Hasegawa M. 1990. Maximum likelihood inference of protein phylogeny and the origin of chloroplasts. J Mol Evol. 31: 151-160.
    • (1990) J Mol Evol. , vol.31 , pp. 151-160
    • Kishino, H.1    Miyata, T.2    Hasegawa, M.3
  • 16
    • 0028177080 scopus 로고
    • A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates
    • Kuhner MK, Felsenstein J. 1994. A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Mol Biol Evol. 11:459-468.
    • (1994) Mol Biol Evol. , vol.11 , pp. 459-468
    • Kuhner, M.K.1    Felsenstein, J.2
  • 18
    • 0034106726 scopus 로고    scopus 로고
    • Appropriate likelihood ratio tests and marginal distributions for evolutionary tree models with constraints on parameters
    • Ota R, Waddell PJ, Hasegawa M, Shimodaira H, Kishino H. 2000. Appropriate likelihood ratio tests and marginal distributions for evolutionary tree models with constraints on parameters. Mol Biol Evol. 17:798-803.
    • (2000) Mol Biol Evol. , vol.17 , pp. 798-803
    • Ota, R.1    Waddell, P.J.2    Hasegawa, M.3    Shimodaira, H.4    Kishino, H.5
  • 20
    • 0036205377 scopus 로고    scopus 로고
    • TREEPUZZLE: Maximum likelihood phylogenetic analysis using quartets and parallel computing
    • Schmidt HA, Strimmer K, Vingron M, von Haesler A. 2002. TREEPUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18:502-504.
    • (2002) Bioinformatics , vol.18 , pp. 502-504
    • Schmidt, H.A.1    Strimmer, K.2    Vingron, M.3    Von Haesler, A.4
  • 21
    • 84907319426 scopus 로고
    • Asymptotic properties of maximum likelihood estimators and likelihood ratio tests under non-standard conditions
    • Self SG, Liang KY. 1987. Asymptotic properties of maximum likelihood estimators and likelihood ratio tests under non-standard conditions. J Am Stat Assoc. 82:605-610.
    • (1987) J Am Stat Assoc. , vol.82 , pp. 605-610
    • Self, S.G.1    Liang, K.Y.2
  • 22
    • 0000472687 scopus 로고
    • Asymptotic distribution of test statistics in the analysis of moment structures under inequality constraints
    • Shapiro A. 1985. Asymptotic distribution of test statistics in the analysis of moment structures under inequality constraints. Biometrika 72: 133-144.
    • (1985) Biometrika , vol.72 , pp. 133-144
    • Shapiro, A.1
  • 23
    • 0036623258 scopus 로고    scopus 로고
    • An approximately unbiased test of phylogenetic tree selection
    • Shimodaira H. 2002. An approximately unbiased test of phylogenetic tree selection. Syst Biol. 5:492-508.
    • (2002) Syst Biol. , vol.5 , pp. 492-508
    • Shimodaira, H.1
  • 24
    • 0032766857 scopus 로고    scopus 로고
    • Multiple comparisons of loglikelihoods with applications to phylogenetic inference
    • Shimodaira H, Hasegawa M. 1999. Multiple comparisons of loglikelihoods with applications to phylogenetic inference. Mol Biol Evol. 16:1114-1116.
    • (1999) Mol Biol Evol. , vol.16 , pp. 1114-1116
    • Shimodaira, H.1    Hasegawa, M.2
  • 25
    • 84890355576 scopus 로고    scopus 로고
    • Likelihood ratio tests with boundary constraints using data-dependent degrees of freedom
    • Susko E. 2013. Likelihood ratio tests with boundary constraints using data-dependent degrees of freedom. Biometrika 100:1019-1023.
    • (2013) Biometrika , vol.100 , pp. 1019-1023
    • Susko, E.1
  • 26
    • 0001336205 scopus 로고    scopus 로고
    • Phylogenetic inference
    • Hillis DM, Moritz C, Mable BK, editors. Sunderland (MA): Sinauer Associates
    • Swofford DL, Olsen GJ, Waddell PJ, Hillis DM. 1996. Phylogenetic inference. In: Hillis DM, Moritz C, Mable BK, editors. Molecular systematics. Sunderland (MA): Sinauer Associates. p. 407-514.
    • (1996) Molecular Systematic , pp. 407-514
    • Swofford, D.L.1    Olsen, G.J.2    Waddell, P.J.3    Hillis, D.M.4
  • 27
    • 0002644952 scopus 로고
    • Maximum likelihood estimation of misspecified models
    • White H. 1982. Maximum likelihood estimation of misspecified models. Econometrica 50:1-25.
    • (1982) Econometrica , vol.50 , pp. 1-25
    • White, H.1
  • 28
    • 0028064845 scopus 로고
    • Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods
    • Yang Z. 1994. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J Mol Evol. 39:306-314.
    • (1994) J Mol Evol. , vol.39 , pp. 306-314
    • Yang, Z.1
  • 29
    • 0030683599 scopus 로고    scopus 로고
    • PAML: A program for phylogenetic analysis by maximum likelihood
    • Yang Z. 1997. PAML: a program for phylogenetic analysis by maximum likelihood. Comput Appl Biosci. 13:555-556.
    • (1997) Comput Appl Biosci. , vol.13 , pp. 555-556
    • Yang, Z.1
  • 30
    • 34547803197 scopus 로고    scopus 로고
    • PAML 4: A program for phylogenetic analysis bymaximum likelihood
    • Yang Z. 2007. PAML 4: a program for phylogenetic analysis bymaximum likelihood. Mol Biol Evol. 24:1586-1591.
    • (2007) Mol Biol Evol. , vol.24 , pp. 1586-1591
    • Yang, Z.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.