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Volumn 24, Issue 1, 2007, Pages 288-293

Performance of a new invariants method on homogeneous and nonhomogeneous quartet trees

Author keywords

Invariants; Markov process; Molecular evolution; Nonhomogenous; Phylogenetic inference; Phylogenetic tree

Indexed keywords

ALGORITHM; ARTICLE; COMPUTER PROGRAM; MATHEMATICAL ANALYSIS; MATHEMATICAL MODEL; PHYLOGENY; SIMULATION;

EID: 33845880639     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msl153     Document Type: Article
Times cited : (36)

References (32)
  • 1
    • 0242607587 scopus 로고    scopus 로고
    • Phylogenetic invariants for the general Markov model of sequence mutation
    • Allman E, Rhodes J. 2003. Phylogenetic invariants for the general Markov model of sequence mutation. Math Biosci. 186(2):113-144.
    • (2003) Math Biosci , vol.186 , Issue.2 , pp. 113-144
    • Allman, E.1    Rhodes, J.2
  • 3
    • 55449086015 scopus 로고    scopus 로고
    • Quartets and parameter recovery for the general Markov model of sequence mutation
    • Allman E, Rhodes J. 2004b. Quartets and parameter recovery for the general Markov model of sequence mutation. Appl Math Res Exp. 2004(4):107-131.
    • (2004) Appl Math Res Exp. 2004 , vol.4 , pp. 107-131
    • Allman, E.1    Rhodes, J.2
  • 4
    • 33745625661 scopus 로고    scopus 로고
    • The identifiability of tree topology for phylogenetic models, including covarion and mixture models
    • Allman E, Rhodes J. 2006. The identifiability of tree topology for phylogenetic models, including covarion and mixture models. J Comput Biol. 13:1101-1113.
    • (2006) J Comput Biol , vol.13 , pp. 1101-1113
    • Allman, E.1    Rhodes, J.2
  • 5
    • 84926074258 scopus 로고    scopus 로고
    • Catalog of small trees
    • Pachter L, Sturmfels B, editors, Chapter 15. Cambridge UK, Cambridge University Press
    • Casanellas M, Garcia L, Sullivant S. 2005. Catalog of small trees. In: Pachter L, Sturmfels B, editors. Algebraic statistics for computational biology. Chapter 15. Cambridge (UK): Cambridge University Press.
    • (2005) Algebraic statistics for computational biology
    • Casanellas, M.1    Garcia, L.2    Sullivant, S.3
  • 6
    • 84926125532 scopus 로고    scopus 로고
    • The strand symmetric model
    • Pachter L, Sturmfels B, editors, Chapter 16. Cambridge UK, Cambridge University Press
    • Casanellas M, Sullivant S. 2005. The strand symmetric model. In: Pachter L, Sturmfels B, editors. Algebraic statistics for computational biology. Chapter 16. Cambridge (UK): Cambridge University Press.
    • (2005) Algebraic statistics for computational biology
    • Casanellas, M.1    Sullivant, S.2
  • 7
    • 0001899693 scopus 로고
    • Invariants of phylogenies in a simple case with discrete states
    • Cavender J, Felsenstein J. 1987. Invariants of phylogenies in a simple case with discrete states. J Classif. 4:57-71.
    • (1987) J Classif , vol.4 , pp. 57-71
    • Cavender, J.1    Felsenstein, J.2
  • 8
    • 33745627269 scopus 로고    scopus 로고
    • Tree construction using singular value decomposition
    • Pachter L, Sturmfels B, editors, Chapter 19. Cambridge UK, Cambridge University Press. p
    • Eriksson N. 2005. Tree construction using singular value decomposition. In: Pachter L, Sturmfels B, editors. Algebraic statistics for computational biology. Chapter 19. Cambridge (UK): Cambridge University Press. p. 347-358.
    • (2005) Algebraic statistics for computational biology , pp. 347-358
    • Eriksson, N.1
  • 9
    • 21144483732 scopus 로고
    • Invariants of some probability models used in phylogenetic inference
    • Evans S, Speed T. 1993. Invariants of some probability models used in phylogenetic inference. Ann Stat. 21:355-377.
    • (1993) Ann Stat , vol.21 , pp. 355-377
    • Evans, S.1    Speed, T.2
  • 10
    • 0019797407 scopus 로고
    • Evolutionary trees from DNA sequences: A maximum likelihood approach
    • Felsenstein J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol. 17:368-376.
    • (1981) J Mol Evol , vol.17 , pp. 368-376
    • Felsenstein, J.1
  • 12
    • 0028932387 scopus 로고
    • Phylogenetic invariants for more general evolutionary models
    • Ferretti V, Sankoff D. 1995. Phylogenetic invariants for more general evolutionary models. J Theor Biol. 147-162.
    • (1995) J Theor Biol , pp. 147-162
    • Ferretti, V.1    Sankoff, D.2
  • 13
    • 0031829758 scopus 로고    scopus 로고
    • Inferring pattern and process: Maximum likelihood implementation of a non-homogeneous model of DNA sequence evolution for phylogenetic analysis
    • Galtier N, Gouy M. 1998. Inferring pattern and process: maximum likelihood implementation of a non-homogeneous model of DNA sequence evolution for phylogenetic analysis. Mol Biol Evol. 154(4):871-879.
    • (1998) Mol Biol Evol , vol.154 , Issue.4 , pp. 871-879
    • Galtier, N.1    Gouy, M.2
  • 14
    • 33845870548 scopus 로고    scopus 로고
    • trees webpage. Available from
    • Garcia LD, Porter J. 2005. Small phylogenetic trees webpage. Available from: http://bio.math.berkeley.edu/ascb/chapter15/.
    • (2005) Small phylogenetic
    • Garcia, L.D.1    Porter, J.2
  • 15
    • 0034617766 scopus 로고    scopus 로고
    • Phylogenetic invariants and geometry
    • Hagedorn T, Landweber L. 2000. Phylogenetic invariants and geometry. J Theor Biol. 205:365-376.
    • (2000) J Theor Biol , vol.205 , pp. 365-376
    • Hagedorn, T.1    Landweber, L.2
  • 16
    • 11944268967 scopus 로고
    • Performance of phylogenetic methods in simulation
    • Huelsenbeck J. 1995. Performance of phylogenetic methods in simulation. Syst Biol. 44:17-48.
    • (1995) Syst Biol , vol.44 , pp. 17-48
    • Huelsenbeck, J.1
  • 17
    • 0025061094 scopus 로고
    • Limitations of the evolutionary parsimony method of phylogenetic analysis
    • Jin L, Nei M. 1990. Limitations of the evolutionary parsimony method of phylogenetic analysis. Mol Biol Evol. 7:82-102.
    • (1990) Mol Biol Evol , vol.7 , pp. 82-102
    • Jin, L.1    Nei, M.2
  • 19
    • 0019296687 scopus 로고
    • A simple method for estimating evolutionary rates of base substitution through comparative studies of nucleotide sequences
    • Kimura M. 1980. A simple method for estimating evolutionary rates of base substitution through comparative studies of nucleotide sequences. J Mol Evol. 16:111-120.
    • (1980) J Mol Evol , vol.16 , pp. 111-120
    • Kimura, M.1
  • 20
    • 0001464973 scopus 로고
    • Estimation of evolutionary sequences between homologous nucleotide sequences
    • Kimura M. 1981. Estimation of evolutionary sequences between homologous nucleotide sequences. Proc Natl Acad Sci USA. 78:454-458.
    • (1981) Proc Natl Acad Sci USA , vol.78 , pp. 454-458
    • Kimura, M.1
  • 21
    • 0023150708 scopus 로고
    • A rate-independent technique for analysis of nucleic acid sequences: Evolutionary parsimony
    • Lake J. 1987. A rate-independent technique for analysis of nucleic acid sequences: evolutionary parsimony. Mol Biol Evol. 4:167-191.
    • (1987) Mol Biol Evol , vol.4 , pp. 167-191
    • Lake, J.1
  • 22
    • 84926122052 scopus 로고    scopus 로고
    • Pachter L, Sturmfels B, editors, Cambridge UK, Cambridge University Press
    • Pachter L, Sturmfels B, editors. 2005. Algebraic statistics for computational biology. Cambridge (UK): Cambridge University Press.
    • (2005) Algebraic statistics for computational biology
  • 23
    • 33845874798 scopus 로고    scopus 로고
    • Paradis E, Strimmer K, Claude J, Jobb G, Opgen-Rhein R, Dutheil J, Noel Y, Bolker B, Lemon J. 2006. Ape: analyses of phylogenetics and evolution. R package version 1.8-3
    • Paradis E, Strimmer K, Claude J, Jobb G, Opgen-Rhein R, Dutheil J, Noel Y, Bolker B, Lemon J. 2006. Ape: analyses of phylogenetics and evolution. R package version 1.8-3.
  • 24
    • 28444445926 scopus 로고    scopus 로고
    • R Development Core Team, Vienna Austria, R Foundation for Statistical Computing
    • R Development Core Team. 2005. R: a language and environment for statistical computing. Vienna (Austria): R Foundation for Statistical Computing.
    • (2005) R: A language and environment for statistical computing
  • 25
    • 0030928378 scopus 로고    scopus 로고
    • Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
    • Rambaut A, Grassly N. 1997. Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput Appl Biosci. 13:235-238.
    • (1997) Comput Appl Biosci , vol.13 , pp. 235-238
    • Rambaut, A.1    Grassly, N.2
  • 26
    • 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(4):406-425.
    • (1987) Mol Biol Evol , vol.4 , Issue.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 27
    • 0032700064 scopus 로고    scopus 로고
    • Phylogenetic invariants for genome rearrangements
    • Sankoff D, Blanchette M. 1999. Phylogenetic invariants for genome rearrangements. J Comput Biol. 6:431-445.
    • (1999) J Comput Biol , vol.6 , pp. 431-445
    • Sankoff, D.1    Blanchette, M.2
  • 28
    • 0001212293 scopus 로고
    • A complete family of phylogenetic invariants for any number of taxa under Kimura's 3ST model
    • Steel M, Székely L, Erdos P, Waddell P. 1993. A complete family of phylogenetic invariants for any number of taxa under Kimura's 3ST model. N Z J Bot. 31:289-296.
    • (1993) N Z J Bot , vol.31 , pp. 289-296
    • Steel, M.1    Székely, L.2    Erdos, P.3    Waddell, P.4
  • 29
    • 15944419142 scopus 로고    scopus 로고
    • Toric ideals of phylogenetic invariants
    • Sturmfels B, Sullivant S. 2005. Toric ideals of phylogenetic invariants. J Comput Biol. 12:204-228.
    • (2005) J Comput Biol , vol.12 , pp. 204-228
    • Sturmfels, B.1    Sullivant, S.2
  • 30
    • 0030683599 scopus 로고    scopus 로고
    • PAML: A program package for phylogenetic analysis by maximum likelihood
    • Yang Z. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci. 15:555-556.
    • (1997) Comput Appl Biosci , vol.15 , pp. 555-556
    • Yang, Z.1
  • 31
    • 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
  • 32
    • 0033004740 scopus 로고    scopus 로고
    • Estimation of the transition/transversion rate bias and species sampling
    • Yang Z, Yoder AD. 1999. Estimation of the transition/transversion rate bias and species sampling. J Mol Evol. 48:274-283.
    • (1999) J Mol Evol , vol.48 , pp. 274-283
    • Yang, Z.1    Yoder, A.D.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.