메뉴 건너뛰기




Volumn 36, Issue , 2005, Pages 541-562

Phylogenomics

Author keywords

Inconsistency; Molecular phylogeny; Systematic bias; Taxon sampling; Tree of life

Indexed keywords

PHYLOGENY;

EID: 27744441025     PISSN: 00664162     EISSN: None     Source Type: Book Series    
DOI: 10.1146/annurev.ecolsys.35.112202.130205     Document Type: Review
Times cited : (271)

References (145)
  • 2
    • 1342309210 scopus 로고    scopus 로고
    • Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference
    • Altekar G, Dwarkadas S, Huelsenbeck JP, Ronquist F. 2004. Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference. Bioinformatics 20:407-15
    • (2004) Bioinformatics , vol.20 , pp. 407-415
    • Altekar, G.1    Dwarkadas, S.2    Huelsenbeck, J.P.3    Ronquist, F.4
  • 4
    • 0037022379 scopus 로고    scopus 로고
    • The analysis of 100 genes supports the grouping of three highly divergent amoebae: Dictyostelium, Entamoeba, and Mastigamoeba
    • Bapteste E, Brinkmann H, Lee JA, Moore DV, Sensen CW, et al. 2002. The analysis of 100 genes supports the grouping of three highly divergent amoebae: Dictyostelium, Entamoeba, and Mastigamoeba. Proc. Natl. Acad. Sci. USA 99:1414-19
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 1414-1419
    • Bapteste, E.1    Brinkmann, H.2    Lee, J.A.3    Moore, D.V.4    Sensen, C.W.5
  • 5
    • 0002844544 scopus 로고
    • Combining trees as a way of combining data sets for phylogenetic inference, and the desirability of combining gene trees
    • Baum BR. 1992. Combining trees as a way of combining data sets for phylogenetic inference, and the desirability of combining gene trees. Taxon 41:3-10
    • (1992) Taxon , vol.41 , pp. 3-10
    • Baum, B.R.1
  • 7
    • 0022743812 scopus 로고
    • A measure of the similarity of sets of sequences not requiring sequence alignment
    • Blaisdell BE. 1986. A measure of the similarity of sets of sequences not requiring sequence alignment. Proc. Natl. Acad. Sci. USA 83:5155-59
    • (1986) Proc. Natl. Acad. Sci. USA , vol.83 , pp. 5155-5159
    • Blaisdell, B.E.1
  • 9
    • 0036143403 scopus 로고    scopus 로고
    • Genome-scale evolution: Reconstructing gene orders in the ancestral species
    • Bourque G, Pevzner PA. 2002. Genome-scale evolution: reconstructing gene orders in the ancestral species. Genome Res. 12:26-36
    • (2002) Genome Res. , vol.12 , pp. 26-36
    • Bourque, G.1    Pevzner, P.A.2
  • 11
    • 0033015732 scopus 로고    scopus 로고
    • Archaea sister group of bacteria? Indications from tree reconstruction artifacts in ancient phylogenies
    • Brinkmann H, Philippe H. 1999. Archaea sister group of bacteria? Indications from tree reconstruction artifacts in ancient phylogenies. Mol. Biol. Evol. 16:817-25
    • (1999) Mol. Biol. Evol. , vol.16 , pp. 817-825
    • Brinkmann, H.1    Philippe, H.2
  • 13
    • 0036137155 scopus 로고    scopus 로고
    • Eubacterial phylogeny based on translational apparatus proteins
    • Brochier C, Bapteste E, Moreira D, Philippe H. 2002. Eubacterial phylogeny based on translational apparatus proteins. Trends Genet. 18:1-5
    • (2002) Trends Genet. , vol.18 , pp. 1-5
    • Brochier, C.1    Bapteste, E.2    Moreira, D.3    Philippe, H.4
  • 14
    • 0037118037 scopus 로고    scopus 로고
    • Phylogeny: A non-hyperthermophilic ancestor for bacteria
    • Brochier C, Philippe H. 2002. Phylogeny: a non-hyperthermophilic ancestor for bacteria. Nature 417:244
    • (2002) Nature , vol.417 , pp. 244
    • Brochier, C.1    Philippe, H.2
  • 15
    • 0037306453 scopus 로고    scopus 로고
    • Ancient horizontal gene transfer
    • Brown JR. 2003. Ancient horizontal gene transfer. Nat. Rev. Genet. 4:121-32
    • (2003) Nat. Rev. Genet. , vol.4 , pp. 121-132
    • Brown, J.R.1
  • 18
    • 10644238478 scopus 로고    scopus 로고
    • Phylogenetic signal in nucleotide data from seed plants: Implications for resolving the seed plant tree of life
    • Burleigh JG, Mathews S. 2004. Phylogenetic signal in nucleotide data from seed plants: implications for resolving the seed plant tree of life. Am. J. Bot. 91:1599-613
    • (2004) Am. J. Bot. , vol.91 , pp. 1599-1613
    • Burleigh, J.G.1    Mathews, S.2
  • 19
    • 2442667671 scopus 로고    scopus 로고
    • A phylogenomic study of endosymbiotic bacteria
    • Canback B, Tamas I, Andersson SG. 2004. A phylogenomic study of endosymbiotic bacteria. Mol. Biol. Evol. 21:1110-22
    • (2004) Mol. Biol. Evol. , vol.21 , pp. 1110-1122
    • Canback, B.1    Tamas, I.2    Andersson, S.G.3
  • 20
    • 2342450579 scopus 로고    scopus 로고
    • Systematic searches for molecular synapomorphies in model metazoan genomes give some support for Ecdysozoa after accounting for the idiosyncrasies of Caenorhabditis elegans
    • Copley RR, Aloy P, Russell RB, Telford MJ. 2004. Systematic searches for molecular synapomorphies in model metazoan genomes give some support for Ecdysozoa after accounting for the idiosyncrasies of Caenorhabditis elegans. Evol. Dev. 6:164-69
    • (2004) Evol. Dev. , vol.6 , pp. 164-169
    • Copley, R.R.1    Aloy, P.2    Russell, R.B.3    Telford, M.J.4
  • 21
    • 0036221248 scopus 로고    scopus 로고
    • When does the incongruence length difference test fail?
    • Darlu P, Lecointre G. 2002. When does the incongruence length difference test fail? Mol. Biol. Evol. 19:432-37
    • (2002) Mol. Biol. Evol. , vol.19 , pp. 432-437
    • Darlu, P.1    Lecointre, G.2
  • 22
    • 0036061865 scopus 로고    scopus 로고
    • A phylogenomic approach to bacterial phylogeny: Evidence of a core of genes sharing a common history
    • Daubin V, Gouy M, Perriere G. 2002. A phylogenomic approach to bacterial phylogeny: evidence of a core of genes sharing a common history. Genome Res. 12:1080-90
    • (2002) Genome Res. , vol.12 , pp. 1080-1090
    • Daubin, V.1    Gouy, M.2    Perriere, G.3
  • 23
    • 0001546577 scopus 로고
    • Separate versus combined analysis of phylogenetic evidence
    • de Queiroz A, Donoghue MJ, Kim J. 1995. Separate versus combined analysis of phylogenetic evidence. Annu. Rev. Ecol. Syst. 26:657-81
    • (1995) Annu. Rev. Ecol. Syst. , vol.26 , pp. 657-681
    • De Queiroz, A.1    Donoghue, M.J.2    Kim, J.3
  • 24
    • 17744394753 scopus 로고    scopus 로고
    • Phylogenomics and the reconstruction of the tree of life
    • Delsuc F, Brinkmann H, Philippe H. 2005. Phylogenomics and the reconstruction of the tree of life. Nat. Rev. Genet. 6:361-75
    • (2005) Nat. Rev. Genet. , vol.6 , pp. 361-375
    • Delsuc, F.1    Brinkmann, H.2    Philippe, H.3
  • 25
    • 0034512402 scopus 로고    scopus 로고
    • Noise and incongruence: Interpreting results of the incongruence length difference test
    • Dolphin K, Belshaw R, Orme CD, Quicke DL. 2000. Noise and incongruence: interpreting results of the incongruence length difference test. Mol. Phylogenet. Evol. 17:401-6
    • (2000) Mol. Phylogenet. Evol. , vol.17 , pp. 401-406
    • Dolphin, K.1    Belshaw, R.2    Orme, C.D.3    Quicke, D.L.4
  • 26
    • 0033603539 scopus 로고    scopus 로고
    • Phylogenetic classification and the universal tree
    • Doolittle WF. 1999. Phylogenetic classification and the universal tree. Science 284:2124-29
    • (1999) Science , vol.284 , pp. 2124-2129
    • Doolittle, W.F.1
  • 27
    • 27844438226 scopus 로고    scopus 로고
    • Genome-scale evidence of the nematode-arthropod clade
    • Dopazo H, Dopazo J. 2005. Genome-scale evidence of the nematode-arthropod clade. Genome Biol. 6:R41
    • (2005) Genome Biol. , vol.6
    • Dopazo, H.1    Dopazo, J.2
  • 28
    • 4944257028 scopus 로고    scopus 로고
    • Phylogenomics and the number of characters required for obtaining an accurate phylogeny of eukaryote model species
    • Dopazo H, Santoyo J, Dopazo J. 2004. Phylogenomics and the number of characters required for obtaining an accurate phylogeny of eukaryote model species. Bioinformatics 20:i116-21
    • (2004) Bioinformatics , vol.20
    • Dopazo, H.1    Santoyo, J.2    Dopazo, J.3
  • 29
    • 0036005517 scopus 로고    scopus 로고
    • Increased congruence does not necessarily indicate increased phylogenetic accuracy - The behavior of the incongruence length difference test in mixed-model analyses
    • Dowton M, Austin AD. 2002. Increased congruence does not necessarily indicate increased phylogenetic accuracy - the behavior of the incongruence length difference test in mixed-model analyses. Syst. Biol. 51:19-31
    • (2002) Syst. Biol. , vol.51 , pp. 19-31
    • Dowton, M.1    Austin, A.D.2
  • 31
    • 28044436397 scopus 로고    scopus 로고
    • Accelerated evolution associated with genome reduction in a free-living prokaryote
    • Dufresne A, Garczarek L, Partensky F. 2005. Accelerated evolution associated with genome reduction in a free-living prokaryote. Genome Biol. 6:R14
    • (2005) Genome Biol. , vol.6
    • Dufresne, A.1    Garczarek, L.2    Partensky, F.3
  • 32
    • 2342492364 scopus 로고    scopus 로고
    • The consistent phylogenetic signal in genome trees revealed by reducing the impact of noise
    • Dutilh BE, Huynen MA, Bruno WJ, Snel B. 2004. The consistent phylogenetic signal in genome trees revealed by reducing the impact of noise. J. Mol. Evol. 58:527-39
    • (2004) J. Mol. Evol. , vol.58 , pp. 527-539
    • Dutilh, B.E.1    Huynen, M.A.2    Bruno, W.J.3    Snel, B.4
  • 33
    • 0036700153 scopus 로고    scopus 로고
    • A genomic schism in birds revealed by phylogenetic analysis of DNA strings
    • Edwards SV, Fertil B, Giron A, Deschavanne PJ. 2002. A genomic schism in birds revealed by phylogenetic analysis of DNA strings. Syst. Biol. 51:599-613
    • (2002) Syst. Biol. , vol.51 , pp. 599-613
    • Edwards, S.V.1    Fertil, B.2    Giron, A.3    Deschavanne, P.J.4
  • 34
    • 0031976258 scopus 로고    scopus 로고
    • Phylogenomics: Improving functional predictions for uncharacterized genes by evolutionary analysis
    • Eisen JA. 1998. Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis. Genome Res. 8:163-67
    • (1998) Genome Res. , vol.8 , pp. 163-167
    • Eisen, J.A.1
  • 36
    • 84959798530 scopus 로고
    • Cases in which parsimony or compatibility methods will be positively misleading
    • Felsenstein J. 1978. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 27:401-10
    • (1978) Syst. Zool. , vol.27 , pp. 401-410
    • Felsenstein, J.1
  • 37
    • 0024152983 scopus 로고
    • Phylogenies from molecular sequences: Inference and reliability
    • Felsenstein J. 1988. Phylogenies from molecular sequences: inference and reliability. Annu. Rev. Genet. 22:521-65
    • (1988) Annu. Rev. Genet. , vol.22 , pp. 521-565
    • Felsenstein, J.1
  • 40
    • 0014800108 scopus 로고
    • Distinguishing homologous from analogous proteins
    • Fitch WM. 1970. Distinguishing homologous from analogous proteins. Syst. Zool. 19:99-113
    • (1970) Syst. Zool. , vol.19 , pp. 99-113
    • Fitch, W.M.1
  • 41
    • 0014860857 scopus 로고
    • An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution
    • Fitch WM, Markowitz E. 1970. An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution. Biochem. Genet. 4:579-93
    • (1970) Biochem. Genet. , vol.4 , pp. 579-593
    • Fitch, W.M.1    Markowitz, E.2
  • 42
    • 0033231209 scopus 로고    scopus 로고
    • Whole genome-based phylogenetic analysis of free-living microorganisms
    • Fitz-Gibbon ST, House CH. 1999. Whole genome-based phylogenetic analysis of free-living microorganisms. Nucleic Acids Res. 27:4218-22
    • (1999) Nucleic Acids Res. , vol.27 , pp. 4218-4222
    • Fitz-Gibbon, S.T.1    House, C.H.2
  • 44
    • 2442449251 scopus 로고    scopus 로고
    • Inconsistencies in arguments for the supertree approach: Supermatrices versus supertrees of Crocodylia
    • Gatesy J, Baker RH, Hayashi C. 2004. Inconsistencies in arguments for the supertree approach: supermatrices versus supertrees of Crocodylia. Syst. Biol. 53:342-55
    • (2004) Syst. Biol. , vol.53 , pp. 342-355
    • Gatesy, J.1    Baker, R.H.2    Hayashi, C.3
  • 45
    • 0242268536 scopus 로고    scopus 로고
    • Evolution: Ending incongruence
    • Gee H. 2003. Evolution: ending incongruence. Nature 425:782
    • (2003) Nature , vol.425 , pp. 782
    • Gee, H.1
  • 46
    • 0027526039 scopus 로고
    • Statistical tests of models of DNA substitution
    • Goldman N. 1993. Statistical tests of models of DNA substitution. J. Mol. Evol. 36:182-98
    • (1993) J. Mol. Evol. , vol.36 , pp. 182-198
    • Goldman, N.1
  • 47
    • 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. 49:652-70
    • (2000) Syst. Biol. , vol.49 , pp. 652-670
    • Goldman, N.1    Anderson, J.P.2    Rodrigo, A.G.3
  • 48
    • 3042683994 scopus 로고    scopus 로고
    • The chloroplast genome of Nymphaea alba: Whole-genome analyses and the problem of identifying the most basal angiosperm
    • Goremykin VV, Hirsch-Ernst KI, Wolfl S, Hellwig FH. 2004. The chloroplast genome of Nymphaea alba: whole-genome analyses and the problem of identifying the most basal angiosperm. Mol. Biol. Evol. 21:1445-54
    • (2004) Mol. Biol. Evol. , vol.21 , pp. 1445-1454
    • Goremykin, V.V.1    Hirsch-Ernst, K.I.2    Wolfl, S.3    Hellwig, F.H.4
  • 49
    • 0032025857 scopus 로고    scopus 로고
    • Is it better to add taxa or characters to a difficult phylogenetic problem?
    • Graybeal A. 1998. Is it better to add taxa or characters to a difficult phylogenetic problem? Syst. Biol. 47:9-17
    • (1998) Syst. Biol. , vol.47 , pp. 9-17
    • Graybeal, A.1
  • 50
    • 3042643735 scopus 로고    scopus 로고
    • Genome phylogenetic analysis based on extended gene contents
    • Gu X, Zhang H. 2004. Genome phylogenetic analysis based on extended gene contents. Mol. Biol. Evol. 21:1401-8
    • (2004) Mol. Biol. Evol. , vol.21 , pp. 1401-1408
    • Gu, X.1    Zhang, H.2
  • 52
    • 14544293086 scopus 로고    scopus 로고
    • Non-homogeneous model of sequence evolution indicates independent origins of primary endosymbionts within the Enterobacteriales (γ-proteobacteria)
    • Herbeck JT, Degnan PH, Wernegreen JJ. 2005. Non-homogeneous model of sequence evolution indicates independent origins of primary endosymbionts within the Enterobacteriales (γ-proteobacteria). Mol. Biol. Evol. 22:520-32
    • (2005) Mol. Biol. Evol. , vol.22 , pp. 520-532
    • Herbeck, J.T.1    Degnan, P.H.2    Wernegreen, J.J.3
  • 53
  • 55
    • 4644252702 scopus 로고    scopus 로고
    • Tracing the decay of the historical signal in biological sequence data
    • Ho SY, Jermiin L. 2004. Tracing the decay of the historical signal in biological sequence data. Syst. Biol. 53:623-37
    • (2004) Syst. Biol. , vol.53 , pp. 623-637
    • Ho, S.Y.1    Jermiin, L.2
  • 56
    • 0037379673 scopus 로고    scopus 로고
    • Phylogeny estimation: Traditional and Bayesian approaches
    • Holder M, Lewis PO. 2003. Phylogeny estimation: traditional and Bayesian approaches. Nat. Rev. Genet. 4:275-84
    • (2003) Nat. Rev. Genet. , vol.4 , pp. 275-284
    • Holder, M.1    Lewis, P.O.2
  • 57
    • 0036218557 scopus 로고    scopus 로고
    • Using homolog groups to create a whole-genomic tree of free-living organisms: An update
    • House CH, Fitz-Gibbon ST. 2002. Using homolog groups to create a whole-genomic tree of free-living organisms: an update. J. Mol. Evol. 54:539-47
    • (2002) J. Mol. Evol. , vol.54 , pp. 539-547
    • House, C.H.1    Fitz-Gibbon, S.T.2
  • 58
    • 0242371470 scopus 로고    scopus 로고
    • Geobiological analysis using whole genome-based tree building applied to the Bacteria, Archaea and Eukarya
    • House CH, Runnegar B, Fitz-Gibbon ST. 2003. Geobiological analysis using whole genome-based tree building applied to the Bacteria, Archaea and Eukarya. Geobiology 1:15-26
    • (2003) Geobiology , vol.1 , pp. 15-26
    • House, C.H.1    Runnegar, B.2    Fitz-Gibbon, S.T.3
  • 59
    • 10344254308 scopus 로고    scopus 로고
    • Trichomonas hydrogenosomes contain the NADH dehydrogenase module of mitochondrial complex I
    • Hrdy I, Hirt RP, Dolezal P, Bardonova L, Foster PG, et al. 2004. Trichomonas hydrogenosomes contain the NADH dehydrogenase module of mitochondrial complex I. Nature 432:618-22
    • (2004) Nature , vol.432 , pp. 618-622
    • Hrdy, I.1    Hirt, R.P.2    Dolezal, P.3    Bardonova, L.4    Foster, P.G.5
  • 60
    • 0030328811 scopus 로고    scopus 로고
    • A likelihood ratio test to detect conflicting phylogenetic signal
    • Huelsenbeck JP, Bull JJ. 1996. A likelihood ratio test to detect conflicting phylogenetic signal. Syst. Biol. 45:92-98
    • (1996) Syst. Biol. , vol.45 , pp. 92-98
    • Huelsenbeck, J.P.1    Bull, J.J.2
  • 61
    • 0032746022 scopus 로고    scopus 로고
    • Disk-covering, a fast-converging method for phylogenetic tree reconstruction
    • Huson DH, Nettles SM, Warnow TJ. 1999. Disk-covering, a fast-converging method for phylogenetic tree reconstruction. J. Comput. Biol. 6:369-86
    • (1999) J. Comput. Biol. , vol.6 , pp. 369-386
    • Huson, D.H.1    Nettles, S.M.2    Warnow, T.J.3
  • 62
    • 4544229161 scopus 로고    scopus 로고
    • Phylogenetic trees based on gene content
    • Huson DH, Steel M. 2004. Phylogenetic trees based on gene content. Bioinformatics 20:2044-49
    • (2004) Bioinformatics , vol.20 , pp. 2044-2049
    • Huson, D.H.1    Steel, M.2
  • 63
    • 3042601821 scopus 로고    scopus 로고
    • Covarion shifts cause a long-branch attraction artifact that unites microsporidia and archaebacteria in EF-1α phylogenies
    • Inagaki Y, Susko E, Fast NM, Roger AJ. 2004. Covarion shifts cause a long-branch attraction artifact that unites microsporidia and archaebacteria in EF-1α phylogenies. Mol. Biol. Evol. 21:1340-49
    • (2004) Mol. Biol. Evol. , vol.21 , pp. 1340-1349
    • Inagaki, Y.1    Susko, E.2    Fast, N.M.3    Roger, A.J.4
  • 65
    • 0030315308 scopus 로고    scopus 로고
    • General inconsistency conditions for maximum parsimony: Effects of branch lengths and increasing numbers of taxa
    • Kim J. 1996. General inconsistency conditions for maximum parsimony: effects of branch lengths and increasing numbers of taxa. Syst. Biol. 45:363-74
    • (1996) Syst. Biol. , vol.45 , pp. 363-374
    • Kim, J.1
  • 66
    • 84959806898 scopus 로고
    • A concern for evidence and a phylogenetic hypothesis of relationships among Epicrates (Boidae, Serpentes)
    • Kluge AG. 1989. A concern for evidence and a phylogenetic hypothesis of relationships among Epicrates (Boidae, Serpentes). Syst. Zool. 38:7-25
    • (1989) Syst. Zool. , vol.38 , pp. 7-25
    • Kluge, A.G.1
  • 67
    • 7244221755 scopus 로고    scopus 로고
    • Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous
    • Kolaczkowski B, Thornton JW. 2004. Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous. Nature 431:980-84
    • (2004) Nature , vol.431 , pp. 980-984
    • Kolaczkowski, B.1    Thornton, J.W.2
  • 68
    • 0036499057 scopus 로고    scopus 로고
    • SHOT: A web server for the construction of genome phylogenies
    • Korbel JO, Snel B, Huynen MA, Bork P. 2002. SHOT: a web server for the construction of genome phylogenies. Trends Genet. 18:158-62
    • (2002) Trends Genet. , vol.18 , pp. 158-162
    • Korbel, J.O.1    Snel, B.2    Huynen, M.A.3    Bork, P.4
  • 69
    • 1842505237 scopus 로고    scopus 로고
    • Deriving the genomic tree of life in the presence of horizontal gene transfer: Conditioned reconstruction
    • Lake JA, Rivera MC. 2004. Deriving the genomic tree of life in the presence of horizontal gene transfer: conditioned reconstruction. Mol. Biol. Evol. 21:681-90
    • (2004) Mol. Biol. Evol. , vol.21 , pp. 681-690
    • Lake, J.A.1    Rivera, M.C.2
  • 70
    • 14544300681 scopus 로고    scopus 로고
    • A Bayesian analysis of metazoan mitochondrial genome arrangements
    • Larget B, Simon DL, Kadane JB, Sweet D. 2005. A Bayesian analysis of metazoan mitochondrial genome arrangements. Mol. Biol. Evol. 22:486-95
    • (2005) Mol. Biol. Evol. , vol.22 , pp. 486-495
    • Larget, B.1    Simon, D.L.2    Kadane, J.B.3    Sweet, D.4
  • 71
    • 2442691520 scopus 로고    scopus 로고
    • A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process
    • Lartillot N, Philippe H. 2004. A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Mol. Biol. Evol. 21:1095-109
    • (2004) Mol. Biol. Evol. , vol.21 , pp. 1095-1109
    • Lartillot, N.1    Philippe, H.2
  • 72
    • 12944281550 scopus 로고    scopus 로고
    • Total evidence requires exclusion of phylogenetically misleading data
    • Lecointre G, Deleporte P. 2005. Total evidence requires exclusion of phylogenetically misleading data. Zool. Ser. 31:101-17
    • (2005) Zool. Ser. , vol.31 , pp. 101-117
    • Lecointre, G.1    Deleporte, P.2
  • 73
    • 0036679128 scopus 로고    scopus 로고
    • The metapopulation genetic algorithm: An efficient solution for the problem of large phylogeny estimation
    • Lemmon AR, Milinkovitch MC. 2002. The metapopulation genetic algorithm: an efficient solution for the problem of large phylogeny estimation. Proc. Natl. Acad. Sci. USA 99:10516-2l
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99
    • Lemmon, A.R.1    Milinkovitch, M.C.2
  • 74
    • 1342271382 scopus 로고    scopus 로고
    • From gene trees to organismal phylogeny in prokaryotes: The case of the γ-proteobacteria
    • Lerat E, Daubin V, Moran NA. 2003. From gene trees to organismal phylogeny in prokaryotes: the case of the γ-proteobacteria. PLoS Biol. 1:101-9
    • (2003) PLoS Biol. , vol.1 , pp. 101-109
    • Lerat, E.1    Daubin, V.2    Moran, N.A.3
  • 75
    • 0033918311 scopus 로고    scopus 로고
    • Whole-genome trees based on the occurrence of folds and orthologs: Implications for comparing genomes on different levels
    • Lin J, Gerstein M. 2000. Whole-genome trees based on the occurrence of folds and orthologs: implications for comparing genomes on different levels. Genome Res. 10:808-18
    • (2000) Genome Res. , vol.10 , pp. 808-818
    • Lin, J.1    Gerstein, M.2
  • 76
    • 0028361182 scopus 로고
    • Recovering evolutionary trees under a more realistic model of sequence evolution
    • Lockhart PJ, Steel MA, Hendy MD, Penny D. 1994. Recovering evolutionary trees under a more realistic model of sequence evolution. Mol. Biol. Evol. 11:605-12
    • (1994) Mol. Biol. Evol. , vol.11 , pp. 605-612
    • Lockhart, P.J.1    Steel, M.A.2    Hendy, M.D.3    Penny, D.4
  • 77
    • 0029935637 scopus 로고    scopus 로고
    • Evolution of chlorophyll and bacteriochlorophyll: The problem of invariant sites in sequence analysis
    • Lockhart PJ, Larkum AWD, Steel MA, Waddell PJ, Penny D. 1996. Evolution of chlorophyll and bacteriochlorophyll: the problem of invariant sites in sequence analysis. Proc. Natl. Acad. Sci. USA 93:1930-34
    • (1996) Proc. Natl. Acad. Sci. USA , vol.93 , pp. 1930-1934
    • Lockhart, P.J.1    Larkum, A.W.D.2    Steel, M.A.3    Waddell, P.J.4    Penny, D.5
  • 78
    • 0032825223 scopus 로고    scopus 로고
    • The root of the tree of life in the light of the covarion model
    • Lopez P, Forterre P, Philippe H. 1999. The root of the tree of life in the light of the covarion model. J. Mol. Evol. 49:496-508
    • (1999) J. Mol. Evol. , vol.49 , pp. 496-508
    • Lopez, P.1    Forterre, P.2    Philippe, H.3
  • 79
    • 0035252569 scopus 로고    scopus 로고
    • Parallel adaptive radiations in two major clades of placental mammals
    • Madsen O, Scally M, Douady CJ, Kao DJ, DeBry RW, et al. 2001. Parallel adaptive radiations in two major clades of placental mammals. Nature 409:610-14
    • (2001) Nature , vol.409 , pp. 610-614
    • Madsen, O.1    Scally, M.2    Douady, C.J.3    Kao, D.J.4    Debry, R.W.5
  • 81
    • 0141832717 scopus 로고    scopus 로고
    • Revisiting the Glires concept-phylogenetic analysis of nuclear sequences
    • Misawa K, Janke A. 2003. Revisiting the Glires concept-phylogenetic analysis of nuclear sequences. Mol. Phylogenet. Evol. 28:320-27
    • (2003) Mol. Phylogenet. Evol. , vol.28 , pp. 320-327
    • Misawa, K.1    Janke, A.2
  • 82
    • 11944269526 scopus 로고
    • Testing species phylogenies and phylogenetic methods with congruence
    • Miyamoto MM, Fitch WM. 1995. Testing species phylogenies and phylogenetic methods with congruence. Syst. Biol. 44:64-76
    • (1995) Syst. Biol. , vol.44 , pp. 64-76
    • Miyamoto, M.M.1    Fitch, W.M.2
  • 86
    • 0000791476 scopus 로고
    • Lengths of chromosomal segments conserved since divergence of man and mouse
    • Nadeau JH, Taylor BA. 1984. Lengths of chromosomal segments conserved since divergence of man and mouse. Proc. Natl. Acad. Sci. USA 81:814-18
    • (1984) Proc. Natl. Acad. Sci. USA , vol.81 , pp. 814-818
    • Nadeau, J.H.1    Taylor, B.A.2
  • 88
    • 0033604476 scopus 로고    scopus 로고
    • Phylogenomics. Ancestral primate viewed
    • O'Brien SJ, Stanyon R. 1999. Phylogenomics. Ancestral primate viewed. Nature 402:365-66
    • (1999) Nature , vol.402 , pp. 365-366
    • O'Brien, S.J.1    Stanyon, R.2
  • 89
    • 0023498406 scopus 로고
    • Earliest phylogenetic branching: Comparing rRNA-based evolutionary trees inferred with various techniques
    • Olsen G. 1987. Earliest phylogenetic branching: comparing rRNA-based evolutionary trees inferred with various techniques. Cold Spring Harbor Symp. Quant. Biol. 52:825-37
    • (1987) Cold Spring Harbor Symp. Quant. Biol. , vol.52 , pp. 825-837
    • Olsen, G.1
  • 90
    • 4243140058 scopus 로고    scopus 로고
    • A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or characterstate data
    • Pagel M, Meade A. 2004. A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or characterstate data. Syst. Biol. 53:571-81
    • (2004) Syst. Biol. , vol.53 , pp. 571-581
    • Pagel, M.1    Meade, A.2
  • 91
    • 17744379783 scopus 로고    scopus 로고
    • The Opisthokonta and the Ecdysozoa may not be clades: Stronger support for the grouping of plant and animal than for animal and fungi and stronger support for the Coelomata than Ecdysozoa
    • Philip GK, Creevey CJ, McInerney JO. 2005. The Opisthokonta and the Ecdysozoa may not be clades: stronger support for the grouping of plant and animal than for animal and fungi and stronger support for the Coelomata than Ecdysozoa. Mol. Biol. Evol. 22:1175-84
    • (2005) Mol. Biol. Evol. , vol.22 , pp. 1175-1184
    • Philip, G.K.1    Creevey, C.J.2    McInerney, J.O.3
  • 92
    • 0242354974 scopus 로고    scopus 로고
    • Horizontal gene transfer and phylogenetics
    • Philippe H, Douady CJ. 2003. Horizontal gene transfer and phylogenetics. Curr. Opin. Microbiol. 6:498-505
    • (2003) Curr. Opin. Microbiol. , vol.6 , pp. 498-505
    • Philippe, H.1    Douady, C.J.2
  • 93
    • 0034019771 scopus 로고    scopus 로고
    • Phylogeny of eukaryotes based on ribosomal RNA: Long-branch attraction and models of sequence evolution
    • Philippe H, Germot A. 2000. Phylogeny of eukaryotes based on ribosomal RNA: long-branch attraction and models of sequence evolution. Mol. Biol. Evol. 17:830-34
    • (2000) Mol. Biol. Evol. , vol.17 , pp. 830-834
    • Philippe, H.1    Germot, A.2
  • 94
    • 17744386162 scopus 로고    scopus 로고
    • Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia
    • Philippe H, Lartillot N, Brinkmann H. 2005. Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia. Mol. Biol. Evol. 22:1246-53
    • (2005) Mol. Biol. Evol. , vol.22 , pp. 1246-1253
    • Philippe, H.1    Lartillot, N.2    Brinkmann, H.3
  • 96
    • 0034702256 scopus 로고    scopus 로고
    • Early-branching or fast-evolving eukaryotes? An answer based on slowly evolving positions
    • Philippe H, Lopez P, Brinkmann H, Budin K, Germot A, et al. 2000. Early-branching or fast-evolving eukaryotes? An answer based on slowly evolving positions. Proc. R. Soc. London Ser. B. 267:1213-21
    • (2000) Proc. R. Soc. London Ser. B. , vol.267 , pp. 1213-1221
    • Philippe, H.1    Lopez, P.2    Brinkmann, H.3    Budin, K.4    Germot, A.5
  • 98
    • 3042550872 scopus 로고    scopus 로고
    • Genome-scale phylogeny and the detection of systematic biases
    • Phillips MJ, Delsuc F, Penny D. 2004. Genome-scale phylogeny and the detection of systematic biases. Mol. Biol. Evol. 21:1455-58
    • (2004) Mol. Biol. Evol. , vol.21 , pp. 1455-1458
    • Phillips, M.J.1    Delsuc, F.2    Penny, D.3
  • 99
    • 12444313041 scopus 로고    scopus 로고
    • Identifying and removing fast-evolving sites using compatibility analysis: An example from the arthropoda
    • Pisani D. 2004. Identifying and removing fast-evolving sites using compatibility analysis: an example from the arthropoda. Syst. Biol. 53:978-89
    • (2004) Syst. Biol. , vol.53 , pp. 978-989
    • Pisani, D.1
  • 100
    • 0037315735 scopus 로고    scopus 로고
    • Evolutionary implications of microbial genome tetranucleotide frequency biases
    • Pride DT, Meinersmann RJ, Wassenaar TM, Blaser MJ. 2003. Evolutionary implications of microbial genome tetranucleotide frequency biases. Genome Res. 13:145-58
    • (2003) Genome Res. , vol.13 , pp. 145-158
    • Pride, D.T.1    Meinersmann, R.J.2    Wassenaar, T.M.3    Blaser, M.J.4
  • 101
    • 1242335920 scopus 로고    scopus 로고
    • Whole proteome prokaryote phylogeny without sequence alignment: A K-string composition approach
    • Qi J, Wang B, Hao BI. 2004. Whole proteome prokaryote phylogeny without sequence alignment: a K-string composition approach. J. Mol. Evol. 58:1-11
    • (2004) J. Mol. Evol. , vol.58 , pp. 1-11
    • Qi, J.1    Wang, B.2    Hao, B.I.3
  • 102
    • 0033604548 scopus 로고    scopus 로고
    • The earliest angiosperms: Evidence from mitochondrial, plastid and nuclear genomes
    • Qiu YL, Lee J, Bernasconi-Quadroni F, Soltis DE, Soltis PS, et al. 1999. The earliest angiosperms: evidence from mitochondrial, plastid and nuclear genomes. Nature 402:404-7
    • (1999) Nature , vol.402 , pp. 404-407
    • Qiu, Y.L.1    Lee, J.2    Bernasconi-Quadroni, F.3    Soltis, D.E.4    Soltis, P.S.5
  • 103
    • 0027104018 scopus 로고
    • Matrix representation in reconstructing phylogenetic relationships among the eukaryotes
    • Ragan MA. 1992. Matrix representation in reconstructing phylogenetic relationships among the eukaryotes. Biosystems 28:47-55
    • (1992) Biosystems , vol.28 , pp. 47-55
    • Ragan, M.A.1
  • 104
    • 0035861990 scopus 로고    scopus 로고
    • Automatic clustering of orthologs and inparalogs from pairwise species comparisons
    • Remm M, Storm CE, Sonnhammer EL. 2001. Automatic clustering of orthologs and inparalogs from pairwise species comparisons. J. Mol. Biol. 314:1041-52
    • (2001) J. Mol. Biol. , vol.314 , pp. 1041-1052
    • Remm, M.1    Storm, C.E.2    Sonnhammer, E.L.3
  • 105
    • 0242365676 scopus 로고    scopus 로고
    • Genome-scale approaches to resolving incongruence in molecular phylogenies
    • Rokas A, Williams BL, King N, Carroll SB. 2003. Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425:798-804
    • (2003) Nature , vol.425 , pp. 798-804
    • Rokas, A.1    Williams, B.L.2    King, N.3    Carroll, S.B.4
  • 106
    • 0041386108 scopus 로고    scopus 로고
    • MrBayes 3: Bayesian phylogenetic inference under mixed models
    • Ronquist F, Huelsenbeck JP. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-74
    • (2003) Bioinformatics , vol.19 , pp. 1572-1574
    • Ronquist, F.1    Huelsenbeck, J.P.2
  • 107
    • 0037291976 scopus 로고    scopus 로고
    • Taxon sampling, bioinformatics, and phylogenomics
    • Rosenberg MS, Kumar S. 2003. Taxon sampling, bioinformatics, and phylogenomics. Syst. Biol. 52:119-24
    • (2003) Syst. Biol. , vol.52 , pp. 119-124
    • Rosenberg, M.S.1    Kumar, S.2
  • 108
    • 15444379114 scopus 로고    scopus 로고
    • Resolution of a deep animal divergence by the pattern of intron conservation
    • Roy SW, Gilbert W. 2005. Resolution of a deep animal divergence by the pattern of intron conservation. Proc. Natl. Acad. Sci. USA 102:4403-8
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 4403-4408
    • Roy, S.W.1    Gilbert, W.2
  • 109
    • 0033583163 scopus 로고    scopus 로고
    • Acoel flatworms: Earliest extant bilaterian Metazoans, not members of Platyhelminthes
    • Ruiz-Trillo I, Riutort M, Littlewood DT, Herniou EA, Baguna J. 1999. Acoel flatworms: earliest extant bilaterian Metazoans, not members of Platyhelminthes. Science 283:1919-23
    • (1999) Science , vol.283 , pp. 1919-1923
    • Ruiz-Trillo, I.1    Riutort, M.2    Littlewood, D.T.3    Herniou, E.A.4    Baguna, J.5
  • 110
    • 0035527401 scopus 로고    scopus 로고
    • Complexity of the likelihood surface for a large DNA dataset
    • Salter LA. 2001. Complexity of the likelihood surface for a large DNA dataset. Syst. Biol. 50:970-78
    • (2001) Syst. Biol. , vol.50 , pp. 970-978
    • Salter, L.A.1
  • 111
    • 0032030505 scopus 로고    scopus 로고
    • Phylogenetic supertrees: Assembling the trees of life
    • Sanderson MJ, Purvis A, Henze C. 1998. Phylogenetic supertrees: assembling the trees of life. Trends Ecol. Evol. 13:105-9
    • (1998) Trends Ecol. Evol. , vol.13 , pp. 105-109
    • Sanderson, M.J.1    Purvis, A.2    Henze, C.3
  • 112
    • 0036926048 scopus 로고    scopus 로고
    • Troubleshooting molecular phylogenetic analyses
    • Sanderson MJ, Shaffer HB. 2002. Troubleshooting molecular phylogenetic analyses. Ann. Rev. Ecol. Syst. 33:49-72
    • (2002) Ann. Rev. Ecol. Syst. , vol.33 , pp. 49-72
    • Sanderson, M.J.1    Shaffer, H.B.2
  • 114
    • 0141666829 scopus 로고
    • Evolution of 5S RNA and the nonrandomness of base replacement
    • Sankoff D, Morel D, Cedergren R. 1973. Evolution of 5S RNA and the nonrandomness of base replacement. Nat. New Biol. 245:232-34
    • (1973) Nat. New Biol. , vol.245 , pp. 232-234
    • Sankoff, D.1    Morel, D.2    Cedergren, R.3
  • 115
    • 1042280957 scopus 로고    scopus 로고
    • Phylogenomic inference of protein molecular function: Advances and challenges
    • Sjolander K. 2004. Phylogenomic inference of protein molecular function: advances and challenges. Bioinformatics 20:170-79
    • (2004) Bioinformatics , vol.20 , pp. 170-179
    • Sjolander, K.1
  • 116
    • 0032900532 scopus 로고    scopus 로고
    • Genome phylogeny based on gene content
    • Snel B, Bork P, Huynen MA. 1999. Genome phylogeny based on gene content. Nat. Genet. 21:108-10
    • (1999) Nat. Genet. , vol.21 , pp. 108-110
    • Snel, B.1    Bork, P.2    Huynen, M.A.3
  • 117
    • 4644350604 scopus 로고    scopus 로고
    • Genome-scale data, angiosperm relationships, and "ending incongruence": A cautionary tale in phylogenetics
    • Soltis DE, Albert VA, Savolainen V, Hilu K, Qiu YL, et al. 2004. Genome-scale data, angiosperm relationships, and "ending incongruence": a cautionary tale in phylogenetics. Trends Plant Sci. 9:477-83
    • (2004) Trends Plant Sci. , vol.9 , pp. 477-483
    • Soltis, D.E.1    Albert, V.A.2    Savolainen, V.3    Hilu, K.4    Qiu, Y.L.5
  • 118
    • 0036800892 scopus 로고    scopus 로고
    • Phylogeny of seed plants based on evidence from eight genes
    • Soltis DE, Soltis PS, Zanis MJ. 2002. Phylogeny of seed plants based on evidence from eight genes. Am. J. Bot. 89:1670-81
    • (2002) Am. J. Bot. , vol.89 , pp. 1670-1681
    • Soltis, D.E.1    Soltis, P.S.2    Zanis, M.J.3
  • 119
    • 0033604619 scopus 로고    scopus 로고
    • Angiosperm phylogeny inferred from multiple genes as a tool for comparative biology
    • Soltis PS, Soltis DE, Chase MW. 1999. Angiosperm phylogeny inferred from multiple genes as a tool for comparative biology. Nature 402:402-4
    • (1999) Nature , vol.402 , pp. 402-404
    • Soltis, P.S.1    Soltis, D.E.2    Chase, M.W.3
  • 120
    • 14644397888 scopus 로고    scopus 로고
    • RAxML-III: A fast program for maximum likelihood-based inference of large phylogenetic trees
    • Stamatakis A, Ludwig T, Meier H. 2005. RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics 21:456-63
    • (2005) Bioinformatics , vol.21 , pp. 456-463
    • Stamatakis, A.1    Ludwig, T.2    Meier, H.3
  • 121
    • 19444384196 scopus 로고    scopus 로고
    • Should phylogenetic models be trying to 'fit an elephant'?
    • Steel M. 2005. Should phylogenetic models be trying to 'fit an elephant'? Trends Genet. 21:307-9
    • (2005) Trends Genet. , vol.21 , pp. 307-309
    • Steel, M.1
  • 122
    • 0034035066 scopus 로고    scopus 로고
    • Parsimony, likelihood, and the role of models in molecular phylogenetics
    • Steel M, Penny D. 2000. Parsimony, likelihood, and the role of models in molecular phylogenetics. Mol. Biol. Evol. 17:839-50
    • (2000) Mol. Biol. Evol. , vol.17 , pp. 839-850
    • Steel, M.1    Penny, D.2
  • 123
    • 10644253746 scopus 로고    scopus 로고
    • Long branch attraction, taxon sampling, and the earliest angiosperms: Amborella or monocots?
    • Stefanovic S, Rice DW, Palmer JD. 2004. Long branch attraction, taxon sampling, and the earliest angiosperms: Amborella or monocots? BMC Evol. Biol. 4:35
    • (2004) BMC Evol. Biol. , vol.4 , pp. 35
    • Stefanovic, S.1    Rice, D.W.2    Palmer, J.D.3
  • 124
    • 0036173130 scopus 로고    scopus 로고
    • Automated ortholog inference from phylogenetic trees and calculation of orthology reliability
    • Storm CE, Sonnhammer EL. 2002. Automated ortholog inference from phylogenetic trees and calculation of orthology reliability. Bioinformatics 18:92-99
    • (2002) Bioinformatics , vol.18 , pp. 92-99
    • Storm, C.E.1    Sonnhammer, E.L.2
  • 125
    • 0242404116 scopus 로고    scopus 로고
    • Hierarchical phylogenetic models for analyzing multipartite sequence data
    • Suchard MA, Kitchen CM, Sinsheimer JS, Weiss RE. 2003. Hierarchical phylogenetic models for analyzing multipartite sequence data. Syst. Biol. 52:649-64
    • (2003) Syst. Biol. , vol.52 , pp. 649-664
    • Suchard, M.A.1    Kitchen, C.M.2    Sinsheimer, J.S.3    Weiss, R.E.4
  • 126
    • 0002529938 scopus 로고
    • When are phylogeny estimates from molecular and morphological data incongruent?
    • ed. MM Miyamoto, J Cracraft, New York: Oxford Univ. Press
    • Swofford DL. 1991. When are phylogeny estimates from molecular and morphological data incongruent? In Phylogenetic Analysis of DNA Sequences, ed. MM Miyamoto, J Cracraft, pp. 295-333. New York: Oxford Univ. Press
    • (1991) Phylogenetic Analysis of DNA Sequences , pp. 295-333
    • Swofford, D.L.1
  • 128
    • 0001336205 scopus 로고    scopus 로고
    • Phylogenetic inference
    • ed. DM Hillis, C Moritz, BK Mable, Sunderland, MA: Sinauer
    • Swofford DL, Olsen GJ, Waddell PJ, Hillis DM. 1996. Phylogenetic inference. In Molecular Systematics, ed. DM Hillis, C Moritz, BK Mable, pp. 407-514. Sunderland, MA: Sinauer
    • (1996) Molecular Systematics , pp. 407-514
    • Swofford, D.L.1    Olsen, G.J.2    Waddell, P.J.3    Hillis, D.M.4
  • 129
    • 0030660581 scopus 로고    scopus 로고
    • A genomic perspective on protein families
    • Tatusov RL, Koonin EV, Lipman DJ. 1997. A genomic perspective on protein families. Science 278:631-37
    • (1997) Science , vol.278 , pp. 631-637
    • Tatusov, R.L.1    Koonin, E.V.2    Lipman, D.J.3
  • 130
    • 0032778047 scopus 로고    scopus 로고
    • The genomic tree as revealed from whole proteome comparisons
    • Tekaia F, Lazcano A, Dujon B. 1999. The genomic tree as revealed from whole proteome comparisons. Genome Res. 9:550-57
    • (1999) Genome Res. , vol.9 , pp. 550-557
    • Tekaia, F.1    Lazcano, A.2    Dujon, B.3
  • 132
    • 0042710797 scopus 로고    scopus 로고
    • Iterative pass optimization of sequence data
    • Wheeler WC. 2003. Iterative pass optimization of sequence data. Cladistics 19:254-60
    • (2003) Cladistics , vol.19 , pp. 254-260
    • Wheeler, W.C.1
  • 133
    • 0042905752 scopus 로고    scopus 로고
    • Missing data, incomplete taxa, and phylogenetic accuracy
    • Wiens JJ. 2003. Missing data, incomplete taxa, and phylogenetic accuracy. Syst. Biol. 52:528-38
    • (2003) Syst. Biol. , vol.52 , pp. 528-538
    • Wiens, J.J.1
  • 134
    • 30344464074 scopus 로고    scopus 로고
    • Can incomplete taxa rescue phylogenetic analyses from long-branch attraction?
    • In press
    • Wiens JJ. 2005. Can incomplete taxa rescue phylogenetic analyses from long-branch attraction? Syst. Biol. In press
    • (2005) Syst. Biol.
    • Wiens, J.J.1
  • 135
    • 0025952777 scopus 로고
    • Archaeal phylogeny: Reexamination of the phylogenetic position of Archaeoglobus fulgidus in light of certain composition-induced artifacts
    • Woese CR, Achenbach L, Rouviere P, Mandelco L. 1991. Archaeal phylogeny: reexamination of the phylogenetic position of Archaeoglobus fulgidus in light of certain composition-induced artifacts. Syst. Appl. Microbiol. 14:364-71
    • (1991) Syst. Appl. Microbiol. , vol.14 , pp. 364-371
    • Woese, C.R.1    Achenbach, L.2    Rouviere, P.3    Mandelco, L.4
  • 137
    • 0348044549 scopus 로고    scopus 로고
    • Genome trees constructed using five different approaches suggest new major bacterial clades
    • Wolf YI, Rogozin IB, Grishin NV, Tatusov RL, Koonin EV. 2001. Genome trees constructed using five different approaches suggest new major bacterial clades. BMC Evol. Biol. 1:8
    • (2001) BMC Evol. Biol. , vol.1 , pp. 8
    • Wolf, Y.I.1    Rogozin, I.B.2    Grishin, N.V.3    Tatusov, R.L.4    Koonin, E.V.5
  • 138
    • 0345874732 scopus 로고    scopus 로고
    • Coelomata and not Ecdysozoa: Evidence from genome-wide phylogenetic analysis
    • Wolf YI, Rogozin IB, Koonin EV. 2004. Coelomata and not Ecdysozoa: evidence from genome-wide phylogenetic analysis. Genome Res. 14:29-36
    • (2004) Genome Res. , vol.14 , pp. 29-36
    • Wolf, Y.I.1    Rogozin, I.B.2    Koonin, E.V.3
  • 140
    • 0029970097 scopus 로고    scopus 로고
    • Maximum-likelihood models for combined analyses of multiple sequence data
    • Yang Z. 1996. Maximum-likelihood models for combined analyses of multiple sequence data. J. Mol. Evol. 42:587-96
    • (1996) J. Mol. Evol. , vol.42 , pp. 587-596
    • Yang, Z.1
  • 141
    • 0035527350 scopus 로고    scopus 로고
    • Failure of the ILD to determine data combinability for slow loris phylogeny
    • Yoder AD, Irwin JA, Payseur BA. 2001. Failure of the ILD to determine data combinability for slow loris phylogeny. Syst. Biol. 50:408-24
    • (2001) Syst. Biol. , vol.50 , pp. 408-424
    • Yoder, A.D.1    Irwin, J.A.2    Payseur, B.A.3
  • 142
    • 0037000637 scopus 로고    scopus 로고
    • Bayesian estimation of the number of inversions in the history of two chromosomes
    • York TL, Durrett R, Nielsen R. 2002. Bayesian estimation of the number of inversions in the history of two chromosomes. J. Comput. Biol. 9:805-18
    • (2002) J. Comput. Biol. , vol.9 , pp. 805-818
    • York, T.L.1    Durrett, R.2    Nielsen, R.3
  • 143
    • 7444241447 scopus 로고    scopus 로고
    • Detecting phylogenetic incongruence using BIONJ: An improvement of the ILD test
    • Zelwer M, Daubin V. 2004. Detecting phylogenetic incongruence using BIONJ: an improvement of the ILD test. Mol. Phylogenet. Evol. 33:687-93
    • (2004) Mol. Phylogenet. Evol. , vol.33 , pp. 687-693
    • Zelwer, M.1    Daubin, V.2
  • 145
    • 15944400987 scopus 로고    scopus 로고
    • Using shared genomic synteny and shared protein functions to enhance the identification of orthologous gene pairs
    • Zheng XH, Lu F, Wang ZY, Zhong F, Hoover J, Mural R. 2004. Using shared genomic synteny and shared protein functions to enhance the identification of orthologous gene pairs. Bioinformatics 21:703-10
    • (2004) Bioinformatics , vol.21 , pp. 703-710
    • Zheng, X.H.1    Lu, F.2    Wang, Z.Y.3    Zhong, F.4    Hoover, J.5    Mural, R.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.