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Volumn 13, Issue 1, 2012, Pages

Surprising results on phylogenetic tree building methods based on molecular sequences

Author keywords

Distance measures; Maximum likelihood; Molecular sequences; Multiple sequence alignments; Phylogenetic trees; Substitution matrices; Tree building methods

Indexed keywords

BUILDING METHODS; DISTANCE MEASURE; MOLECULAR SEQUENCES; MULTIPLE SEQUENCE ALIGNMENTS; PHYLOGENETIC TREES;

EID: 84862729639     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-13-148     Document Type: Article
Times cited : (11)

References (57)
  • 1
    • 0002331493 scopus 로고
    • Molecular disease, evolution, and genetic heterogeneity
    • Academic Press, New, York, NY, Bryson V, Vogel HJ
    • Zuckerkandl E, Pauling L. Molecular disease, evolution, and genetic heterogeneity. Horizons in Biochemistry 1962, 189-225. Academic Press, New, York, NY, Bryson V, Vogel HJ.
    • (1962) Horizons in Biochemistry , pp. 189-225
    • Zuckerkandl, E.1    Pauling, L.2
  • 3
    • 0036846746 scopus 로고    scopus 로고
    • The origin and evolution of model organisms
    • Hedges S. The origin and evolution of model organisms. Nature Rev Genet 2002, 3(11):838-849.
    • (2002) Nature Rev Genet , vol.3 , Issue.11 , pp. 838-849
    • Hedges, S.1
  • 5
    • 70449527786 scopus 로고    scopus 로고
    • Using non-homogeneous models of nucleotide substitution to identify host shift events: application to the origin of the 1918 Spanish influenza pandemic virus
    • 10.1007/s00239-009-9282-x, 2772961, 19787384
    • dos Reis M, Hay AJ, Goldstein RA. Using non-homogeneous models of nucleotide substitution to identify host shift events: application to the origin of the 1918 Spanish influenza pandemic virus. J Mol Evol 2009, 69(4):333-345. 10.1007/s00239-009-9282-x, 2772961, 19787384.
    • (2009) J Mol Evol , vol.69 , Issue.4 , pp. 333-345
    • dos Reis, M.1    Hay, A.J.2    Goldstein, R.A.3
  • 6
    • 0035823244 scopus 로고    scopus 로고
    • The origin and control of pandemic Influenza
    • 10.1126/science.1063817, 11546857
    • Laver G, Garman E. The origin and control of pandemic Influenza. Science 2001, 293(5536):1776. 10.1126/science.1063817, 11546857.
    • (2001) Science , vol.293 , Issue.5536 , pp. 1776
    • Laver, G.1    Garman, E.2
  • 7
    • 25144472531 scopus 로고    scopus 로고
    • Phylogenetic diversity and the greedy algorithm
    • 10.1080/10635150590947023, 16051588
    • Steel M. Phylogenetic diversity and the greedy algorithm. Syst Biol 2005, 54(4):527. 10.1080/10635150590947023, 16051588.
    • (2005) Syst Biol , vol.54 , Issue.4 , pp. 527
    • Steel, M.1
  • 8
    • 64049089255 scopus 로고    scopus 로고
    • Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation
    • 10.1002/humu.20921, 18853457
    • Van Oven M, Kayser M. Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Human Mutation 2009, 30(2):E386-E394. 10.1002/humu.20921, 18853457.
    • (2009) Human Mutation , vol.30 , Issue.2
    • Van Oven, M.1    Kayser, M.2
  • 9
    • 0037803577 scopus 로고    scopus 로고
    • The study of structured populations-new hope for a difficult and divided science
    • 10.1038/nrg1112, 12838345
    • Hey J, Machado C. The study of structured populations-new hope for a difficult and divided science. Nature Rev Genet 2003, 4(7):535-543. 10.1038/nrg1112, 12838345.
    • (2003) Nature Rev Genet , vol.4 , Issue.7 , pp. 535-543
    • Hey, J.1    Machado, C.2
  • 10
    • 0347532847 scopus 로고    scopus 로고
    • Applying the bootstrap in phylogeny reconstruction
    • Soltis P, Soltis D. Applying the bootstrap in phylogeny reconstruction. Stat Sci 2003, 18(2):256-267.
    • (2003) Stat Sci , vol.18 , Issue.2 , pp. 256-267
    • Soltis, P.1    Soltis, D.2
  • 11
    • 0029526909 scopus 로고
    • Objections to bootstrapping phylogenies: a critique
    • Sanderson M. Objections to bootstrapping phylogenies: a critique. Syst Biol 1995, 44(3):299.
    • (1995) Syst Biol , vol.44 , Issue.3 , pp. 299
    • Sanderson, M.1
  • 12
    • 33846491679 scopus 로고    scopus 로고
    • A Phylogenomic study of human, dog and mouse
    • 10.1371/journal.pcbi.0030002, 1761043, 17206860
    • Cannarozzi GM, Schneider A, Gonnet GH. A Phylogenomic study of human, dog and mouse. PLoS Comput Biol 2007, 3(1):e2. 10.1371/journal.pcbi.0030002, 1761043, 17206860.
    • (2007) PLoS Comput Biol , vol.3 , Issue.1
    • Cannarozzi, G.M.1    Schneider, A.2    Gonnet, G.H.3
  • 13
    • 0035527406 scopus 로고    scopus 로고
    • Bias in Phylogenetic Estimation and Its Relevance to the Choice between Parsimony and Likelihood Methods
    • Swofford DL, Waddell PJ, Huelsenbeck JP, Foster PG, Lewis PO, Rogers JS. Bias in Phylogenetic Estimation and Its Relevance to the Choice between Parsimony and Likelihood Methods. Syst Biol 2001, 50(4):525-539.
    • (2001) Syst Biol , vol.50 , Issue.4 , pp. 525-539
    • Swofford, D.L.1    Waddell, P.J.2    Huelsenbeck, J.P.3    Foster, P.G.4    Lewis, P.O.5    Rogers, J.S.6
  • 14
    • 22844452772 scopus 로고    scopus 로고
    • Branch-length prior influences bayesian posterior probability of phylogeny
    • 10.1080/10635150590945313, 16012111
    • Yang Z, Rannala B. Branch-length prior influences bayesian posterior probability of phylogeny. Syst Biol 2005, 54(3):455-470. 10.1080/10635150590945313, 16012111.
    • (2005) Syst Biol , vol.54 , Issue.3 , pp. 455-470
    • Yang, Z.1    Rannala, B.2
  • 15
    • 33745256005 scopus 로고    scopus 로고
    • Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative
    • 10.1080/10635150600755453, 16785212
    • Anisimova M, Gascuel O. Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative. Syst Biol 2006, 55(4):539-52. 10.1080/10635150600755453, 16785212.
    • (2006) Syst Biol , vol.55 , Issue.4 , pp. 539-552
    • Anisimova, M.1    Gascuel, O.2
  • 16
    • 80052014395 scopus 로고    scopus 로고
    • Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes
    • 10.1093/sysbio/syr041, 3158332, 21540409
    • Anisimova M, Gil M, Dufayard JF, Dessimoz C, Gascuel O. Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes. Syst Biol 2011, 60(5):685-699. 10.1093/sysbio/syr041, 3158332, 21540409.
    • (2011) Syst Biol , vol.60 , Issue.5 , pp. 685-699
    • Anisimova, M.1    Gil, M.2    Dufayard, J.F.3    Dessimoz, C.4    Gascuel, O.5
  • 17
    • 0019424782 scopus 로고
    • Comparison of Phylogenetic Trees
    • Robinson DF, Foulds LR. Comparison of Phylogenetic Trees. Math Biosci 1981, 53(1-2):131-147.
    • (1981) Math Biosci , vol.53 , Issue.1-2 , pp. 131-147
    • Robinson, D.F.1    Foulds, L.R.2
  • 18
    • 84874615468 scopus 로고    scopus 로고
    • Evaluating sequence alignments and phylogenies: new methods and large-scale comparisons
    • PhD thesis, ETH Zurich2010. [Diss. ETH No. 19261]
    • Gil M. Evaluating sequence alignments and phylogenies: new methods and large-scale comparisons. PhD thesis, ETH Zurich2010. [Diss. ETH No. 19261] http://www.ncbi.nlm.nih.gov/Taxonomy/.
    • Gil, M.1
  • 19
    • 77950538424 scopus 로고    scopus 로고
    • Phylogenetic assessment of alignments reveals neglected tree signal in gaps
    • 10.1186/gb-2010-11-4-r37, 2884540, 20370897
    • Dessimoz C, Gil M. Phylogenetic assessment of alignments reveals neglected tree signal in gaps. Genome Biol 2010, 11(4):R37. 10.1186/gb-2010-11-4-r37, 2884540, 20370897.
    • (2010) Genome Biol , vol.11 , Issue.4
    • Dessimoz, C.1    Gil, M.2
  • 21
    • 78651316211 scopus 로고    scopus 로고
    • OMA 2011: orthology inference among 1000 complete genomes
    • 3013747, 21113020, Database issue
    • Altenhoff AM, Schneider A, Gonnet GH, Dessimoz C. OMA 2011: orthology inference among 1000 complete genomes. Nucleic Acids Res 2011, 39(Database issue):D289-D294. 3013747, 21113020.
    • (2011) Nucleic Acids Res , vol.39
    • Altenhoff, A.M.1    Schneider, A.2    Gonnet, G.H.3    Dessimoz, C.4
  • 22
    • 0014757386 scopus 로고
    • A general method applicable to the search for similarities in the amino acid sequence of two proteins
    • 10.1016/0022-2836(70)90057-4, 5420325
    • Needleman SB, Wunsch CD. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 1970, 48:443-453. 10.1016/0022-2836(70)90057-4, 5420325.
    • (1970) J Mol Biol , vol.48 , pp. 443-453
    • Needleman, S.B.1    Wunsch, C.D.2
  • 24
    • 0014800108 scopus 로고
    • Distinguishing homologous from analogous proteins
    • 10.2307/2412448, 5449325
    • Fitch WM. Distinguishing homologous from analogous proteins. Syst Zool 1970, 19(2):99-113. 10.2307/2412448, 5449325.
    • (1970) Syst Zool , vol.19 , Issue.2 , pp. 99-113
    • Fitch, W.M.1
  • 25
    • 59149097358 scopus 로고    scopus 로고
    • The algorithm of OMA for large-scale orthology inference
    • Roth AC, Gonnet GH, Dessimoz C. The algorithm of OMA for large-scale orthology inference. BMC Bioinf 2008, 9:518.
    • (2008) BMC Bioinf , vol.9 , pp. 518
    • Roth, A.C.1    Gonnet, G.H.2    Dessimoz, C.3
  • 26
    • 59149102602 scopus 로고    scopus 로고
    • Phylogenetic and functional assessment of orthologs inference projects and methods
    • 10.1371/journal.pcbi.1000262, 2612752, 19148271
    • Altenhoff AM, Dessimoz C. Phylogenetic and functional assessment of orthologs inference projects and methods. PLoS Comput Biol 2009, 5:e1000262. 10.1371/journal.pcbi.1000262, 2612752, 19148271.
    • (2009) PLoS Comput Biol , vol.5
    • Altenhoff, A.M.1    Dessimoz, C.2
  • 27
    • 73649209034 scopus 로고
    • Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature
    • 10.1016/S0022-2836(62)80066-7, 14470099
    • Marmur J, Doty P. Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature*. J Mol Biol 1962, 5:109-118. 10.1016/S0022-2836(62)80066-7, 14470099.
    • (1962) J Mol Biol , vol.5 , pp. 109-118
    • Marmur, J.1    Doty, P.2
  • 28
    • 0027968068 scopus 로고
    • CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice
    • 10.1093/nar/22.22.4673, 308517, 7984417
    • Thompson J, Higgins D, Gibson T. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994, 22:4673-4680. 10.1093/nar/22.22.4673, 308517, 7984417.
    • (1994) Nucleic Acids Res , vol.22 , pp. 4673-4680
    • Thompson, J.1    Higgins, D.2    Gibson, T.3
  • 30
    • 0037100671 scopus 로고    scopus 로고
    • MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
    • 10.1093/nar/gkf436, 135756, 12136088
    • Katoh K, Misawa K, Kuma K, Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 2002, 30(14):3059. 10.1093/nar/gkf436, 135756, 12136088.
    • (2002) Nucleic Acids Res , vol.30 , Issue.14 , pp. 3059
    • Katoh, K.1    Misawa, K.2    Kuma, K.3    Miyata, T.4
  • 31
    • 13744252890 scopus 로고    scopus 로고
    • MAFFT version 5: improvement in accuracy of multiple sequence alignment
    • 10.1093/nar/gki198, 548345, 15661851
    • Katoh K, Kuma K, Toh H, Miyata T. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res 2005, 33(2):511-518. 10.1093/nar/gki198, 548345, 15661851.
    • (2005) Nucleic Acids Res , vol.33 , Issue.2 , pp. 511-518
    • Katoh, K.1    Kuma, K.2    Toh, H.3    Miyata, T.4
  • 32
    • 0036203448 scopus 로고    scopus 로고
    • Multiple sequence alignment using partial order graphs
    • 10.1093/bioinformatics/18.3.452, 11934745
    • Lee C, Grasso C, Sharlow M. Multiple sequence alignment using partial order graphs. Bioinformatics 2002, 18(3):452-464. 10.1093/bioinformatics/18.3.452, 11934745.
    • (2002) Bioinformatics , vol.18 , Issue.3 , pp. 452-464
    • Lee, C.1    Grasso, C.2    Sharlow, M.3
  • 33
    • 46249095233 scopus 로고    scopus 로고
    • Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis
    • 10.1126/science.1158395, 18566285
    • Loytynoja A, Goldman N. Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis. Science 2008, 320(5883):1632-1635. 10.1126/science.1158395, 18566285.
    • (2008) Science , vol.320 , Issue.5883 , pp. 1632-1635
    • Loytynoja, A.1    Goldman, N.2
  • 35
    • 84866489365 scopus 로고    scopus 로고
    • Probabilistic ancestral sequences based on the Markovian Model of Evolution - algorithms and applications
    • Oxford University Press, , Liberles DA
    • Cannarozzi GM, Schneider A, Gonnet GH. Probabilistic ancestral sequences based on the Markovian Model of Evolution - algorithms and applications. Ancestral Sequence Reconstruction 2007, Oxford University Press, , Liberles DA.
    • (2007) Ancestral Sequence Reconstruction
    • Cannarozzi, G.M.1    Schneider, A.2    Gonnet, G.H.3
  • 36
    • 0034073452 scopus 로고    scopus 로고
    • Darwin v. 2.0: An Interpreted Computer Language for the Biosciences
    • 10.1093/bioinformatics/16.2.101, 10842729
    • Gonnet GH, Hallett MT, Korostensky C, Bernardin L. Darwin v. 2.0: An Interpreted Computer Language for the Biosciences. Bioinformatics 2000, 16(2):101-103. 10.1093/bioinformatics/16.2.101, 10842729.
    • (2000) Bioinformatics , vol.16 , Issue.2 , pp. 101-103
    • Gonnet, G.H.1    Hallett, M.T.2    Korostensky, C.3    Bernardin, L.4
  • 37
    • 14644430471 scopus 로고    scopus 로고
    • ProbCons: probabilistic consistency-based multiple sequence alignment
    • 10.1101/gr.2821705, 546535, 15687296
    • Do C, Mahabhashyam M, Brudno M, Batzoglou S. ProbCons: probabilistic consistency-based multiple sequence alignment. Genome Res 2005, 15(2):330. 10.1101/gr.2821705, 546535, 15687296.
    • (2005) Genome Res , vol.15 , Issue.2 , pp. 330
    • Do, C.1    Mahabhashyam, M.2    Brudno, M.3    Batzoglou, S.4
  • 38
    • 0242578620 scopus 로고    scopus 로고
    • A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
    • 10.1080/10635150390235520, 14530136
    • Guindon S, Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 2003, 52(5):696-704. 10.1080/10635150390235520, 14530136.
    • (2003) Syst Biol , vol.52 , Issue.5 , pp. 696-704
    • Guindon, S.1    Gascuel, O.2
  • 39
    • 77950806408 scopus 로고    scopus 로고
    • New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0
    • 10.1093/sysbio/syq010, 20525638
    • Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 2010, 59(3):307-21. 10.1093/sysbio/syq010, 20525638.
    • (2010) Syst Biol , vol.59 , Issue.3 , pp. 307-321
    • Guindon, S.1    Dufayard, J.F.2    Lefort, V.3    Anisimova, M.4    Hordijk, W.5    Gascuel, O.6
  • 40
    • 45849154166 scopus 로고    scopus 로고
    • An improved general amino acid replacement matrix
    • 10.1093/molbev/msn067, 18367465
    • Le S, Gascuel O. An improved general amino acid replacement matrix. Mol Biol Evol 2008, 25(7):1307. 10.1093/molbev/msn067, 18367465.
    • (2008) Mol Biol Evol , vol.25 , Issue.7 , pp. 1307
    • Le, S.1    Gascuel, O.2
  • 41
    • 33750403801 scopus 로고    scopus 로고
    • RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
    • 10.1093/bioinformatics/btl446, 16928733
    • Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006, 22(21):2688-2690. 10.1093/bioinformatics/btl446, 16928733.
    • (2006) Bioinformatics , vol.22 , Issue.21 , pp. 2688-2690
    • Stamatakis, A.1
  • 43
    • 0026691182 scopus 로고
    • The rapid generation of mutation data matrices from protein sequences
    • Jones DT, Taylor WR, Thornton JM. The rapid generation of mutation data matrices from protein sequences. Comput Applic Biosci 1992, 8:275-282.
    • (1992) Comput Applic Biosci , vol.8 , pp. 275-282
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 44
    • 0026656815 scopus 로고
    • Exhaustive matching of the entire protein sequence database
    • Gonnet GH, Cohen MA, Benner SA. Exhaustive matching of the entire protein sequence database. Science 1992, 256(5003):1443-1445.
    • (1992) Science , vol.256 , Issue.5003 , pp. 1443-1445
    • Gonnet, G.H.1    Cohen, M.A.2    Benner, S.A.3
  • 45
    • 0035031966 scopus 로고    scopus 로고
    • A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach
    • 10.1093/oxfordjournals.molbev.a003851, 11319253
    • Whelan S, Goldman N. A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol Biol Evol 2001, 18(5):691-699. 10.1093/oxfordjournals.molbev.a003851, 11319253.
    • (2001) Mol Biol Evol , vol.18 , Issue.5 , pp. 691-699
    • Whelan, S.1    Goldman, N.2
  • 46
    • 0019887799 scopus 로고
    • Identification of common molecular subsequences
    • 10.1016/0022-2836(81)90087-5, 7265238
    • Smith TF, Waterman MS. Identification of common molecular subsequences. J Mol Biol 1981, 147:195-197. 10.1016/0022-2836(81)90087-5, 7265238.
    • (1981) J Mol Biol , vol.147 , pp. 195-197
    • Smith, T.F.1    Waterman, M.S.2
  • 47
    • 0027483434 scopus 로고
    • Empirical and structural models for insertions and deletions in the divergent evolution of proteins
    • 10.1006/jmbi.1993.1105, 8445636
    • Benner SA, Cohen MA, Gonnet GH. Empirical and structural models for insertions and deletions in the divergent evolution of proteins. J Mol Biol 1993, 229(4):1065-1082. 10.1006/jmbi.1993.1105, 8445636.
    • (1993) J Mol Biol , vol.229 , Issue.4 , pp. 1065-1082
    • Benner, S.A.1    Cohen, M.A.2    Gonnet, G.H.3
  • 49
    • 0030807655 scopus 로고    scopus 로고
    • BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data
    • 10.1093/oxfordjournals.molbev.a025808, 9254330
    • Gascuel O. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. Mol Biol Evol 1997, 14(7):685-695. 10.1093/oxfordjournals.molbev.a025808, 9254330.
    • (1997) Mol Biol Evol , vol.14 , Issue.7 , pp. 685-695
    • Gascuel, O.1
  • 50
    • 43349096191 scopus 로고    scopus 로고
    • Getting a tree fast: Neighbor Joining, FastME, and distance-based methods
    • Desper R, Gascuel O. Getting a tree fast: Neighbor Joining, FastME, and distance-based methods. Curr Protoc Bioinf 2006, Chapter 6:Unit 6.3.
    • (2006) Curr Protoc Bioinf , vol.Chapter 6
    • Desper, R.1    Gascuel, O.2
  • 51
    • 0014211361 scopus 로고
    • The construction of phylogenetic trees
    • 10.1126/science.155.3760.279, 5334057
    • Fitch W, Margoliash E. The construction of phylogenetic trees. Science 1967, 155:279-284. 10.1126/science.155.3760.279, 5334057.
    • (1967) Science , vol.155 , pp. 279-284
    • Fitch, W.1    Margoliash, E.2
  • 52
    • 0023375195 scopus 로고
    • The neighbor-joining method: a new method for reconstructing phylogenetic trees
    • Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987, 4(4):406-425.
    • (1987) Mol Biol Evol , vol.4 , Issue.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 54
    • 84874018544 scopus 로고    scopus 로고
    • The NCBI Taxonomy Homepage
    • NCBI
    • NCBI The NCBI Taxonomy Homepage. http://www.ncbi.nlm.nih.gov/Taxonomy/, NCBI.
  • 55
    • 84874635881 scopus 로고    scopus 로고
    • Integrated Taxonomic Information System on-line database
    • ITIS
    • ITIS Integrated Taxonomic Information System on-line database. http://www.itis.gov, ITIS.
  • 57
    • 0026872189 scopus 로고
    • Analyzing algorithms by simulation: variance reduction techniques and simulation speedups
    • McGeoch CC. Analyzing algorithms by simulation: variance reduction techniques and simulation speedups. ACM Comput Surv 1992, 24(2):195-212.
    • (1992) ACM Comput Surv , vol.24 , Issue.2 , pp. 195-212
    • McGeoch, C.C.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.