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Volumn 60, Issue 1, 2011, Pages 74-86

Two stationary nonhomogeneous Markov models of nucleotide sequence evolution

Author keywords

Invariable sites; maximum likelihood; nucleotide substitution model; phylogenetics; reversible nonhomogeneous model; stationary nonhomogeneous model

Indexed keywords

ANIMAL; ARTICLE; BIOLOGICAL MODEL; CLASSIFICATION; COMPUTER SIMULATION; GENETICS; HOMINID; HYLOBATES; MACACA; MOLECULAR EVOLUTION; NUCLEOTIDE SEQUENCE; PHYLOGENY; PROBABILITY;

EID: 79952134572     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1093/sysbio/syq076     Document Type: Article
Times cited : (25)

References (25)
  • 1
    • 33646892649 scopus 로고    scopus 로고
    • Matched-pairs tests of homogeneity with applications to homologous nucleotide sequences
    • DOI 10.1093/bioinformatics/btl064
    • Ababneh F., Jermiin L. S., Ma C., Robinson J. 2006. Matched-pairs tests of homogeneity with applications to homologous nucleotide sequences. Bioinformatics. 22:1225-1231. (Pubitemid 43779015)
    • (2006) Bioinformatics , vol.22 , Issue.10 , pp. 1225-1231
    • Ababneh, F.1    Jermiin, L.S.2    Ma, C.3    Robinson, J.4
  • 2
    • 33646876774 scopus 로고    scopus 로고
    • Generation of the exact distribution and simulation of matched nucleotide sequences on a phylogenetic tree
    • DOI 10.1007/s10852-005-9017-y
    • Ababneh F., Jermiin L. S., Robinson J. 2006. Generation of the exact distribution and simulation of matched nucleotide sequences on a phylogenetic tree. J. Math. Model. Algor. 5:291-308. (Pubitemid 43848159)
    • (2006) Journal of Mathematical Modelling and Algorithms , vol.5 , Issue.3 , pp. 291-308
    • Ababneh, F.1    Jermiin, L.S.2    Robinson, J.3
  • 3
    • 0016355478 scopus 로고
    • New look at statistical-model identification
    • Akaike H. 1974. New look at statistical-model identification. IEEE Trans. Automat. Contr. AC19:716-723.
    • (1974) IEEE Trans. Automat. Contr , vol.AC19 , pp. 716-723
    • Akaike, H.1
  • 4
    • 84972510219 scopus 로고
    • Statistical analysis of hominoid molecular evolution
    • Barry D., Hartigan J. A. 1987. Statistical analysis of hominoid molecular evolution. Stat. Sci. 2:191-210.
    • (1987) Stat. Sci. , vol.2 , pp. 191-210
    • Barry, D.1    Hartigan, J.A.2
  • 5
    • 0001499322 scopus 로고
    • A test for symmetry in contingency table
    • Bowker A. H. 1948. A test for symmetry in contingency table. J. Am. Stat. Assoc. 43:572-574.
    • (1948) J. Am. Stat. Assoc. , vol.43 , pp. 572-574
    • Bowker, A.H.1
  • 6
    • 8744307994 scopus 로고    scopus 로고
    • Multimodel inference: Understanding AIC and BIC in model selection
    • DOI 10.1177/0049124104268644
    • Burnham K. P., Anderson D. A. 2004. Multimodel inference: understanding AIC and BIC in model selection. Sociol. Methods Res. 33:261-304. (Pubitemid 39519124)
    • (2004) Sociological Methods and Research , vol.33 , Issue.2 , pp. 261-304
    • Burnham, K.P.1    Anderson, D.R.2
  • 7
    • 0002629270 scopus 로고
    • Maximum likelihood from incomplete data via an EM algorithm
    • Dempster A. P., Laird N. M., Rubin D. B. 1977. Maximum likelihood from incomplete data via an EM algorithm. J. R. Stat. Soc. B. 39:1-38.
    • (1977) J. R. Stat. Soc. B. , vol.39 , pp. 1-38
    • Dempster, A.P.1    Laird, N.M.2    Rubin, D.B.3
  • 8
    • 53249100490 scopus 로고    scopus 로고
    • Non-homogeneous models of sequence evolution in the Bio++ suite of libraries and programs
    • Dutheil J., Boussau B. 2008. Non-homogeneous models of sequence evolution in the Bio++ suite of libraries and programs. BMC Evol. Biol. 8:255.
    • (2008) BMC Evol. Biol. , vol.8 , pp. 255
    • Dutheil, J.1    Boussau, B.2
  • 9
    • 3242701529 scopus 로고    scopus 로고
    • Modelling compositional heterogeneity
    • Foster P. G. 2004. Modelling compositional heterogeneity. Syst. Biol. 53:485-495.
    • (2004) Syst. Biol. , vol.53 , pp. 485-495
    • Foster, P.G.1
  • 10
    • 0031829758 scopus 로고    scopus 로고
    • Inferring pattern and process: Maximum-likelihood implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic analysis
    • Galtier N., Gouy M. 1998. Inferring pattern and process: maximumlikelihood implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic analysis. Mol. Biol. Evol. 15:871-879. (Pubitemid 28321885)
    • (1998) Molecular Biology and Evolution , vol.15 , Issue.7 , pp. 871-879
    • Galtier, N.1    Gouy, M.2
  • 11
    • 0033534584 scopus 로고    scopus 로고
    • A nonhyperthermophilic common ancestor to extant life forms
    • Galtier N., Tourasse N., Gouy M. 1999. A nonhyperthermophilic common ancestor to extant life forms. Science. 283:220-221.
    • (1999) Science , vol.283 , pp. 220-221
    • Galtier, N.1    Tourasse, N.2    Gouy, M.3
  • 13
    • 33947532595 scopus 로고    scopus 로고
    • Estimation of phylogeny and invariant sites under the general Markov model of nucleotide sequence evolution
    • DOI 10.1080/10635150701247921, PII 773634848
    • Jayaswal V., Robinson J., Jermiin L. S. 2007. Estimation of phylogeny and invariant sites under the general Markov model of nucleotide sequence evolution. Syst. Biol. 56:155-162. (Pubitemid 46474673)
    • (2007) Systematic Biology , vol.56 , Issue.2 , pp. 155-162
    • Jayaswal, V.1    Robinson, J.2    Jermiin, L.3
  • 15
    • 0009199173 scopus 로고
    • The imbedding problem for finite Markov chains
    • Kingman J. F. C. 1962. The imbedding problem for finite Markov chains. Z. Wahrscheinlichkeitstheorie. 1:14-24.
    • (1962) Z. Wahrscheinlichkeitstheorie , vol.1 , pp. 14-24
    • Kingman, J.F.C.1
  • 16
    • 34250944089 scopus 로고
    • Zur theorie der Markoffschen ketten
    • Kolmogoroff A. 1936. Zur theorie der Markoffschen ketten. Math. Annal. 112:155-160.
    • (1936) Math. Annal , vol.112 , pp. 155-160
    • Kolmogoroff, A.1
  • 19
    • 0000776754 scopus 로고
    • On the problem of the most efficient tests of statistical hypotheses
    • Neyman J., Pearson E. S. 1933. On the problem of the most efficient tests of statistical hypotheses. Philos. Trans. R. Soc. Lond. A. 231:289-337.
    • (1933) Philos. Trans. R. Soc. Lond. A , vol.231 , pp. 289-337
    • Neyman, J.1    Pearson, E.S.2
  • 20
    • 14544271005 scopus 로고    scopus 로고
    • Catarrhine primate divergence dates estimated from complete mitochondrial genomes: Concordance with fossil and nuclear DNA evidence
    • DOI 10.1016/j.jhevol.2004.11.007, PII S0047248404001666
    • Raaum R. L., Sterner K. N., Noviello C. M., Stewart C., Disotell T. R. 2005. Catarrhine primate divergence dates estimated from complete mitochondrial genomes: concordance with fossil and nuclear DNA evidence. J. Human Evol. 48:237-257. (Pubitemid 40301117)
    • (2005) Journal of Human Evolution , vol.48 , Issue.3 , pp. 237-257
    • Raaum, R.L.1    Sterner, K.N.2    Noviello, C.M.3    Stewart, C.-B.4    Disotell, T.R.5
  • 21
    • 0036623258 scopus 로고    scopus 로고
    • An approximately unbiased test of phylogenetic tree selection
    • DOI 10.1080/10635150290069913
    • Shimodaira H. 2002. An approximately unbiased test of phylogenetic tree selection. Syst. Biol. 51:492-508. (Pubitemid 35180700)
    • (2002) Systematic Biology , vol.51 , Issue.3 , pp. 492-508
    • Shimodaira, H.1
  • 22
    • 0036139287 scopus 로고    scopus 로고
    • CONSEL: For assessing the confidence of phylogenetic tree selection
    • Shimodaira H., Hasegawa M. 2001. CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics. 17:1246-1247. (Pubitemid 33735360)
    • (2001) Bioinformatics , vol.17 , Issue.12 , pp. 1246-1247
    • Shimodaira, H.1    Hasegawa, M.2
  • 23
    • 84981981465 scopus 로고
    • A test for homogeneity of the marginal distributions in a two-way classification
    • Stuart A. 1955. A test for homogeneity of the marginal distributions in a two-way classification. Biometrika. 42:412-416.
    • (1955) Biometrika , vol.42 , pp. 412-416
    • Stuart, A.1
  • 24
    • 0037388876 scopus 로고    scopus 로고
    • Testing substitution models within a phylogenetic tree
    • DOI 10.1093/molbev/msg073
    • Weiss G., von Haeseler A. 2003. Testing substitution models within a phylogenetic tree. Mol. Biol. Evol. 20:572-578. (Pubitemid 36437907)
    • (2003) Molecular Biology and Evolution , vol.20 , Issue.4 , pp. 572-578
    • Weiss, G.1    Von Haeselert, A.2
  • 25
    • 0028961933 scopus 로고
    • On the use of nucleic acid sequences to infer early branchings in the tree of life
    • Yang Z., Roberts D. 1995. On the use of nucleic acid sequences to infer early branchings in the tree of life. Mol. Biol. Evol. 12:451-458.
    • (1995) Mol. Biol. Evol. , vol.12 , pp. 451-458
    • Yang, Z.1    Roberts, D.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.