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Volumn 61, Issue 4, 2012, Pages 579-593

Phylogenetic inference via sequential monte carlo

Author keywords

Bayesian inference; sequential Monte Carlo

Indexed keywords

RNA 16S;

EID: 84862900415     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1093/sysbio/syr131     Document Type: Article
Times cited : (65)

References (57)
  • 1
    • 1342309210 scopus 로고    scopus 로고
    • Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference
    • DOI 10.1093/bioinformatics/btg427
    • Altekar G., Dwarkadas S., Huelsenbeck J.P., Ronquist F. 2004. Parallel Metropolis coupled Markov chain Monte carlo for Bayesian phylogenetic inference. Bioinformatics. 20:407-415. (Pubitemid 38262773)
    • (2004) Bioinformatics , vol.20 , Issue.3 , pp. 407-415
    • Altekar, G.1    Dwarkadas, S.2    Huelsenbeck, J.P.3    Ronquist, F.4
  • 3
    • 0036964474 scopus 로고    scopus 로고
    • Approximate Bayesian computation in population genetics
    • Beaumont M.A., Zhang W., Balding D.J. 2002. Approximate Bayesian computation in population genetics. Genetics. 162:2025-2035. (Pubitemid 36114682)
    • (2002) Genetics , vol.162 , Issue.4 , pp. 2025-2035
    • Beaumont, M.A.1    Zhang, W.2    Balding, D.J.3
  • 8
    • 0036504051 scopus 로고    scopus 로고
    • A survey of convergence results on particle filtering methods for practitioners
    • DOI 10.1109/78.984773, PII S1053587X02013284
    • Crisan D., Doucet A. 2002. A survey of convergence results on particle filtering for practitioners. IEEE Trans. Signal Process. 50:736-746. (Pubitemid 34295113)
    • (2002) IEEE Transactions on Signal Processing , vol.50 , Issue.3 , pp. 736-746
    • Crisan, D.1    Doucet, A.2
  • 9
    • 0040175723 scopus 로고
    • Markoff chains-denumerable case
    • Doob J.L. 1945. Markoff chains-denumerable case. Trans. Amer. Math. Soc. 58:455-473.
    • (1945) Trans. Amer. Math. Soc. , vol.58 , pp. 455-473
    • Doob, J.L.1
  • 10
    • 49349102500 scopus 로고    scopus 로고
    • Limit theorems for weighted samples with applications to sequential Monte Carlo methods
    • Douc R., Moulines E. 2008. Limit theorems for weighted samples with applications to sequential Monte Carlo methods. Ann. Stat. 36:2344-2376.
    • (2008) Ann. Stat. , vol.36 , pp. 2344-2376
    • Douc, R.1    Moulines, E.2
  • 14
    • 78650500247 scopus 로고    scopus 로고
    • Choosing among partition models in Bayesian phylogenetics
    • Fan Y., Wu R., Chen M.-H., Kuo L., Lewis P.O. 2011. Choosing among partition models in Bayesian phylogenetics. Mol. Biol. Evol. 28:523-532.
    • (2011) Mol. Biol. Evol. , vol.28 , pp. 523-532
    • Fan, Y.1    Wu, R.2    Chen, M.-H.3    Kuo, L.4    Lewis, P.O.5
  • 15
    • 0015808083 scopus 로고
    • Maximum-likelihood estimation of evolutionary trees from continuous characters
    • Felsenstein J. 1973. Maximum-likelihood estimation of evolutionary trees from continuous characters. Am. J. Hum. Genet. 25:471-492.
    • (1973) Am. J. Hum. Genet. , vol.25 , pp. 471-492
    • Felsenstein, J.1
  • 16
    • 0019797407 scopus 로고
    • Evolutionary trees from DNA sequences: A maximum likelihood approach
    • DOI 10.1007/BF01734359
    • Felsenstein J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17:368-376. (Pubitemid 11016207)
    • (1981) Journal of Molecular Evolution , vol.17 , Issue.6 , pp. 368-376
    • Felsenstein, J.1
  • 19
    • 0000736067 scopus 로고    scopus 로고
    • Simulating normalizing constants: From importance sampling to bridge sampling to path sampling
    • Gelman A., Meng X.-L. 1998. Simulating normalizing constants: from importance sampling to bridge sampling to path sampling. Stat. Sci. 13:163-185. (Pubitemid 128466008)
    • (1998) Statistical Science , vol.13 , Issue.2 , pp. 163-185
    • Gelman, A.1    Meng, X.-L.2
  • 20
    • 84858767158 scopus 로고    scopus 로고
    • An efficient sequential Monte-Carlo algorithm for coalescent clustering
    • Red Hook (NY): Curran Associates
    • Grur D., Teh Y.W. 2008. An efficient sequential Monte-Carlo algorithm for coalescent clustering. In: Advances in neural information processing. Red Hook (NY): Curran Associates. p. 521-528.
    • (2008) Advances in Neural Information Processing , pp. 521-528
    • Grur, D.1    Teh, Y.W.2
  • 21
    • 0001129760 scopus 로고    scopus 로고
    • Monte Carlo inference methods in population genetics
    • Griffiths R.C., Tavar S. 1996. Monte Carlo inference methods in population genetics. Math. Comput. Model. 23:141-158. (Pubitemid 126656507)
    • (1996) Mathematical and Computer Modelling , vol.23 , Issue.8-9 , pp. 141-158
    • Griffiths, R.C.1    Tavare, S.2
  • 22
    • 0034077901 scopus 로고    scopus 로고
    • A compound Poisson process for relaxing the molecular clock
    • Huelsenbeck J.P., Larget B., Swofford D. 2000. A compound Poisson process for relaxing the molecular clock. Genetics. 154: 1879-1892. (Pubitemid 30211265)
    • (2000) Genetics , vol.154 , Issue.4 , pp. 1879-1892
    • Huelsenbeck, J.P.1    Larget, B.2    Swofford, D.3
  • 23
    • 0034849408 scopus 로고    scopus 로고
    • MRBAYES: Bayesian inference of phylogenetic trees
    • Huelsenbeck J.P., Ronquist F. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics. 17:754-755. (Pubitemid 32851390)
    • (2001) Bioinformatics , vol.17 , Issue.8 , pp. 754-755
    • Huelsenbeck, J.P.1    Ronquist, F.2
  • 24
    • 0035861456 scopus 로고    scopus 로고
    • Bayesian inference of phylogeny and its impact on evolutionary biology
    • DOI 10.1126/science.1065889
    • Huelsenbeck J.P., Ronquist F., Nielsen R., Bollback J.P. 2001. Bayesian inference of phylogeny and its impact on evolutionary biology. Science. 294:2310-2314. (Pubitemid 33140548)
    • (2001) Science , vol.294 , Issue.5550 , pp. 2310-2314
    • Huelsenbeck, J.P.1    Ronquist, F.2    Nielsen, R.3    Bollback, J.P.4
  • 25
    • 3142712394 scopus 로고    scopus 로고
    • Importance sampling on coalescent histories
    • Iorio M.D., Griffiths R.C. 2004. Importance sampling on coalescent histories. Adv. Appl. Probab. 36:417-433.
    • (2004) Adv. Appl. Probab. , vol.36 , pp. 417-433
    • Iorio, M.D.1    Griffiths, R.C.2
  • 26
    • 16344387501 scopus 로고    scopus 로고
    • DPRml: Distributed phylogeny reconstruction by maximum likelihood
    • DOI 10.1093/bioinformatics/bti100
    • Keane T.M., Naughton T.J., Travers S.A.A., McInerney J.O., McCormack G.P. 2005. DPRml: distributed phylogeny reconstruction by maximum likelihood. Bioinformatics. 21:969-974. (Pubitemid 40467917)
    • (2005) Bioinformatics , vol.21 , Issue.7 , pp. 969-974
    • Keane, T.M.1    Naughton, T.J.2    Travers, S.A.A.3    McInerney, J.O.4    McCormack, G.P.5
  • 27
    • 0019296687 scopus 로고
    • A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
    • DOI 10.1007/BF01731581
    • Kimura M. 1980. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16:111-120. (Pubitemid 11166431)
    • (1980) Journal of Molecular Evolution , vol.16 , Issue.2 , pp. 111-120
    • Kimura, M.1
  • 28
    • 0030304310 scopus 로고    scopus 로고
    • Monte Carlo filter and smoother for non-Gaussian nonlinear state space models
    • Kitagawa G. 1996. Monte Carlo filter and smoother for non-Gaussian nonlinear state space models. J. Comput. Graph. Stat. 5:1-25.
    • (1996) J. Comput. Graph. Stat. , vol.5 , pp. 1-25
    • Kitagawa, G.1
  • 29
    • 84950943564 scopus 로고
    • Sequential imputations and Bayesian missing data problems
    • Kong A., Liu J.S., Wong W.H. 1994. Sequential imputations and Bayesian missing data problems. J. Am. Stat. Assoc. 89:278-288.
    • (1994) J. Am. Stat. Assoc. , vol.89 , pp. 278-288
    • Kong, A.1    Liu, J.S.2    Wong, W.H.3
  • 30
    • 0028177080 scopus 로고
    • A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates
    • Kuhner M.K., 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
  • 32
    • 33644826560 scopus 로고    scopus 로고
    • Computing Bayes factors using thermodynamic integration
    • DOI 10.1080/10635150500433722, PII G4465276345678
    • Lartillot N., Philippe H. 2006. Computing Bayes factors using thermodynamic integration. Syst. Biol. 55:195-207. (Pubitemid 43355101)
    • (2006) Systematic Biology , vol.55 , Issue.2 , pp. 195-207
    • Lartillot, N.1    Philippe, H.2
  • 34
    • 0442309554 scopus 로고    scopus 로고
    • The multiple-try method and local optimization in Metropolis sampling
    • Liu J.S., Liang F., Wong W.H. 2000. The multiple-try method and local optimization in Metropolis sampling. J. Am. Stat. Assoc. 95:121-134.
    • (2000) J. Am. Stat. Assoc. , vol.95 , pp. 121-134
    • Liu, J.S.1    Liang, F.2    Wong, W.H.3
  • 38
    • 84856592816 scopus 로고    scopus 로고
    • On adaptive resampling strategies for sequential Monte Carlo methods
    • Moral P.D., Doucet A., Jasra A. 2012. On adaptive resampling strategies for sequential Monte Carlo methods. Bernoulli. 12:252-278.
    • (2012) Bernoulli. , vol.12 , pp. 252-278
    • Moral, P.D.1    Doucet, A.2    Jasra, A.3
  • 39
    • 21444452127 scopus 로고    scopus 로고
    • Sampling from multimodal distributions using tempered transitions
    • Neal R.M. 1996. Sampling from multimodal distributions using tempered transitions. Stat. Comput. 6:353-366.
    • (1996) Stat. Comput. , vol.6 , pp. 353-366
    • Neal, R.M.1
  • 41
    • 79955434528 scopus 로고    scopus 로고
    • An accurate sequentially Markov conditional sampling distribution for the coalescent with recombination
    • Paul J.S., Steinr ucken M., Song Y.S. 2011. An accurate sequentially Markov conditional sampling distribution for the coalescent with recombination. Genetics. 187:1115-1128.
    • (2011) Genetics. , vol.187 , pp. 1115-1128
    • Paul, J.S.1    Steinr Ucken, M.2    Song, Y.S.3
  • 42
    • 0034777365 scopus 로고    scopus 로고
    • Mathematical elegance with biochemical realism: The covarion model of molecular evolution
    • DOI 10.1007/s002390010258
    • Penny D., McComish B.J., Charleston M.A., Hendy M.D. 2001. Mathematical elegance with biochemical realism: the covarion model of molecular evolution. J. Mol. Evol. 53:711-723. (Pubitemid 32989425)
    • (2001) Journal of Molecular Evolution , vol.53 , Issue.6 , pp. 711-723
    • Penny, D.1    McComish, B.J.2    Charleston, M.A.3    Hendy, M.D.4
  • 43
    • 0029818407 scopus 로고    scopus 로고
    • Probability distribution of molecular evolutionary trees: A new method of phylogenetic inference
    • Rannala B., Yang Z. 1996. Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference. J. Mol. Evol. 43:304-311. (Pubitemid 26315133)
    • (1996) Journal of Molecular Evolution , vol.43 , Issue.3 , pp. 304-311
    • Rannala, B.1    Yang, Z.2
  • 44
    • 22844450838 scopus 로고    scopus 로고
    • Joint bayesian estimation of alignment and phylogeny
    • DOI 10.1080/10635150590947041
    • Redelings B., Suchard M. 2005. Joint Bayesian estimation of alignment and phylogeny. Syst. Biol. 54:401-418. (Pubitemid 41040440)
    • (2005) Systematic Biology , vol.54 , Issue.3 , pp. 401-418
    • Redelings, B.D.1    Suchard, M.A.2
  • 45
    • 25444510807 scopus 로고    scopus 로고
    • Evolutionary models for insertions and deletions in a probabilistic modeling framework
    • Rivas E. 2005. Evolutionary models for insertions and deletions in a probabilistic modeling framework. BMC Bioinformatics. 6:63.
    • (2005) BMC Bioinformatics. , vol.6 , pp. 63
    • Rivas, E.1
  • 47
    • 0019424782 scopus 로고
    • Comparison of phylogenetic trees
    • DOI 10.1016/0025-5564(81)90043-2
    • Robinson D.F., Foulds L.R. 1981. Comparison of phylogenetic trees. Math. Biosci. 33:131-147. (Pubitemid 11129084)
    • (1981) Mathematical Biosciences , vol.53 , Issue.1-2 , pp. 131-147
    • Robinson, D.F.1    Foulds, L.R.2
  • 48
    • 0023375195 scopus 로고
    • The neighbor-joining method: A new method for reconstructing phylogenetic trees
    • Saitou N., Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
    • (1987) Mol. Biol. Evol. , vol.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 50
    • 1542510106 scopus 로고    scopus 로고
    • Phylogenetic estimation of context-dependent substitution rates by maximum likelihood
    • DOI 10.1093/molbev/msh039
    • Siepel A., Haussler D. 2004. Phylogenetic estimation of contextdependent substitution rates by maximum likelihood. Mol. Biol. Evol. 21:468-488. (Pubitemid 38339664)
    • (2004) Molecular Biology and Evolution , vol.21 , Issue.3 , pp. 468-488
    • Siepel, A.1    Haussler, D.2
  • 51
    • 65649118549 scopus 로고    scopus 로고
    • Many-core algorithms for statistical phylogenetics
    • Suchard M.A., Rambaut A. 2009. Many-core algorithms for statistical phylogenetics. Bioinformatics. 25:1370-1376.
    • (2009) Bioinformatics. , vol.25 , pp. 1370-1376
    • Suchard, M.A.1    Rambaut, A.2
  • 52
    • 35949020425 scopus 로고
    • Replica Monte Carlo simulation of spin glasses
    • Swendsen R.H., Wang J.S. 1986. Replica Monte Carlo simulation of spin glasses. Phys. Rev. Lett. 57:2607-2609.
    • (1986) Phys. Rev. Lett. , vol.57 , pp. 2607-2609
    • Swendsen, R.H.1    Wang, J.S.2
  • 53
    • 0002671410 scopus 로고
    • Some probabilistic and statistical problems in the analysis of DNA sequences
    • Tavar S. 1986. Some probabilistic and statistical problems in the analysis of DNA sequences. Lect. Math. Life Sci. 17:57-86.
    • (1986) Lect. Math. Life Sci. , vol.17 , pp. 57-86
    • Tavar, S.1
  • 55
    • 0031741182 scopus 로고    scopus 로고
    • Estimating the rate of evolution of the rate of molecular evolution
    • Thorne J.L., Kishino H., Painter I.S. 1998. Estimating the rate of evolution of the rate of molecular evolution. Mol. Biol. Evol. 15:1647-1657. (Pubitemid 28550989)
    • (1998) Molecular Biology and Evolution , vol.15 , Issue.12 , pp. 1647-1657
    • Thorne, J.L.1    Kishino, H.2    Painter, I.S.3
  • 56
    • 84858068293 scopus 로고    scopus 로고
    • Reuse, recycle, reweigh: Combating influenza through efficient sequential Bayesian computation for massive data
    • Tom J.A., Sinsheimer J.S., Suchard M.A. 2010. Reuse, recycle, reweigh: combating influenza through efficient sequential Bayesian computation for massive data. Ann. Appl. Stat. 4:1722-1748.
    • (2010) Ann. Appl. Stat. , vol.4 , pp. 1722-1748
    • Tom, J.A.1    Sinsheimer, J.S.2    Suchard, M.A.3
  • 57
    • 79951566251 scopus 로고    scopus 로고
    • Improving marginal likelihood estimation for Bayesian phylogenetic model selection
    • Xie W., Lewis P.O., Fan Y., Kuo L., Chen M.-H. 2011. Improving marginal likelihood estimation for Bayesian phylogenetic model selection. Syst. Biol. 60:150-160.
    • (2011) Syst. Biol. , vol.60 , pp. 150-160
    • Xie, W.1    Lewis, P.O.2    Fan, Y.3    Kuo, L.4    Chen, M.-H.5


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