메뉴 건너뛰기




Volumn 24, Issue 3, 2008, Pages 372-384

Incorporation of gap characters and lineage-specific regions into phylogenetic analyses of gene families from divergent clades: An example from the kinesin superfamily across eukaryotes

Author keywords

[No Author keywords available]

Indexed keywords

BAYESIAN ANALYSIS; CLADISTICS; EUKARYOTE; GENE; PARSIMONY ANALYSIS; PHYLOGENETICS;

EID: 43549084185     PISSN: 07483007     EISSN: 10960031     Source Type: Journal    
DOI: 10.1111/j.1096-0031.2007.00183.x     Document Type: Article
Times cited : (7)

References (97)
  • 2
    • 0032233179 scopus 로고    scopus 로고
    • Phylogenetic utility of the external transcribed spacer (ETS) of 18S-26S rDNA: Congruence of ETS and ITS trees of Calycadenia (Compositae)
    • Baldwin, B.G., Markos, S., 1998. Phylogenetic utility of the external transcribed spacer (ETS) of 18S-26S rDNA: congruence of ETS and ITS trees of Calycadenia (Compositae). Mol. Phylogenet. Evol. 10, 449 463.
    • (1998) Mol. Phylogenet. Evol. , vol.10 , pp. 449-463
    • Baldwin, B.G.1    Markos, S.2
  • 3
    • 0036273056 scopus 로고    scopus 로고
    • The potential value of indels as phylogenetic markers: Position of trichomonads as a case study
    • Bapteste, E., Philippe, H., 2002. The potential value of indels as phylogenetic markers: position of trichomonads as a case study. Mol. Biol. Evol. 19, 972 977.
    • (2002) Mol. Biol. Evol. , vol.19 , pp. 972-977
    • Bapteste, E.1    Philippe, H.2
  • 4
    • 0028017447 scopus 로고
    • Molecular phylogenies and how to code insertion/deletion events
    • Barriel, V., 1994. Molecular phylogenies and how to code insertion/deletion events. Life Sci. 317, 693 701.
    • (1994) Life Sci. , vol.317 , pp. 693-701
    • Barriel, V.1
  • 5
    • 0028093739 scopus 로고
    • A phylogenetic analysis of Epilobium (Onagraceae) based on nuclear ribosomal DNA sequences
    • Baum, D.A., Sytsma, K.J., Hoch, P.C., 1994. A phylogenetic analysis of Epilobium (Onagraceae) based on nuclear ribosomal DNA sequences. Syst. Bot. 19, 363 388.
    • (1994) Syst. Bot. , vol.19 , pp. 363-388
    • Baum, D.A.1    Sytsma, K.J.2    Hoch, P.C.3
  • 6
    • 0032088444 scopus 로고    scopus 로고
    • Evolution of annual species of the genus Medicago: A molecular phylogenetic approach
    • Bena, G., Prosper, J.-M., Lejeune, B., Olivieri, I., 1998. Evolution of annual species of the genus Medicago: a molecular phylogenetic approach. Mol. Phylogenet. Evol. 9, 552 559.
    • (1998) Mol. Phylogenet. Evol. , vol.9 , pp. 552-559
    • Bena, G.1    Prosper, J.-M.2    Lejeune, B.3    Olivieri, I.4
  • 8
    • 0031773261 scopus 로고    scopus 로고
    • Substitution bias, rapid saturation, and the use of mtDNA for nematode systematics
    • Blouin, M.S., Yowell, C.A., Courtney, C.H., Dame, J.B., 1998. Substitution bias, rapid saturation, and the use of mtDNA for nematode systematics. Mol. Biol. Evol. 15, 1719 1727.
    • (1998) Mol. Biol. Evol. , vol.15 , pp. 1719-1727
    • Blouin, M.S.1    Yowell, C.A.2    Courtney, C.H.3    Dame, J.B.4
  • 9
    • 0034043778 scopus 로고    scopus 로고
    • Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis
    • Castresana, J., 2000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17, 540 552.
    • (2000) Mol. Biol. Evol. , vol.17 , pp. 540-552
    • Castresana, J.1
  • 10
    • 0042069655 scopus 로고    scopus 로고
    • Comparing bootstrap and posterior probability values in the four-taxon case
    • Cummings, M.P., Handley, S.A., Myers, D.S., Reed, D.L., Rokas, A., Winka, K., 2003. Comparing bootstrap and posterior probability values in the four-taxon case. Syst. Biol. 52, 477 487.
    • (2003) Syst. Biol. , vol.52 , pp. 477-487
    • Cummings, M.P.1    Handley, S.A.2    Myers, D.S.3    Reed, D.L.4    Rokas, A.5    Winka, K.6
  • 11
    • 0033085021 scopus 로고    scopus 로고
    • The virtues of gaps: Xenarthran (Edentate) monophyly supported by a unique deletion in aA-crystallin
    • van Dijk, M.A.M., Paradis, E., Catzeflis, F., de Jong, W.W., 1999. The virtues of gaps: Xenarthran (Edentate) monophyly supported by a unique deletion in aA-crystallin. Syst. Biol. 48, 94 106.
    • (1999) Syst. Biol. , vol.48 , pp. 94-106
    • Van Dijk, A.M.1    Paradis, E.2    Catzeflis, F.3    De Jong, W.W.4
  • 12
    • 9144243812 scopus 로고    scopus 로고
    • The Anopheles gambiae glutathione transferase supergene family: Annotation, phylogeny and expression profiles
    • Ding, Y., Ortelli, F., Rossiter, L.C., Hemingway, J., Ranson, H., 2003. The Anopheles gambiae glutathione transferase supergene family: annotation, phylogeny and expression profiles. BMC Genomics 4, 35.
    • (2003) BMC Genomics , vol.4 , pp. 35
    • Ding, Y.1    Ortelli, F.2    Rossiter, L.C.3    Hemingway, J.4    Ranson, H.5
  • 13
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: Multiple sequence alignment with high accuracy and high throughput
    • Edgar, R.C., 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 22, 1792 1797.
    • (2004) Nucleic Acids Res. , vol.22 , pp. 1792-1797
    • Edgar, R.C.1
  • 15
    • 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, 401 410.
    • (1978) Syst. Zool. , vol.27 , pp. 401-410
    • Felsenstein, J.1
  • 16
    • 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
  • 17
    • 0023084055 scopus 로고
    • Progressive sequence alignment as a prerequisite to correct phylogenetic trees
    • Feng, D.-F., Doolittle, R.F., 1987. Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J. Mol. Evol. 25, 351 360.
    • (1987) J. Mol. Evol. , vol.25 , pp. 351-360
    • Feng, D.-F.1    Doolittle, R.F.2
  • 18
    • 0034789422 scopus 로고    scopus 로고
    • Analysis of mitochondrial nad1b-c intron sequences in Orchidaceae: Utility and coding of length-change characters
    • Freudenstein, J.V., Chase, M.W., 2001. Analysis of mitochondrial nad1b-c intron sequences in Orchidaceae: Utility and coding of length-change characters. Syst. Bot. 26, 643 657.
    • (2001) Syst. Bot. , vol.26 , pp. 643-657
    • Freudenstein, J.V.1    Chase, M.W.2
  • 20
    • 0036593395 scopus 로고    scopus 로고
    • Ancient phylogenetic relationships
    • Gribaldo, S., Philippe, H., 2002. Ancient phylogenetic relationships. Theor. Popul. Biol. 61, 391 408.
    • (2002) Theor. Popul. Biol. , vol.61 , pp. 391-408
    • Gribaldo, S.1    Philippe, H.2
  • 21
    • 0035756272 scopus 로고    scopus 로고
    • The branching order and phylogenetic placement of species from completed bacterial genomes, based on conserved indels found in various proteins
    • Gupta, R.S., 2001. The branching order and phylogenetic placement of species from completed bacterial genomes, based on conserved indels found in various proteins. Int. Microbiol. 4, 187 202.
    • (2001) Int. Microbiol. , vol.4 , pp. 187-202
    • Gupta, R.S.1
  • 22
    • 0028346242 scopus 로고
    • Molecular evolution of noncoding regions of the chloroplast genome in the Crassulaceae and related species
    • van Ham, R.C.H.J., Hart, H., Mes, T.H.M., Sandbrink, J.M., 1994. Molecular evolution of noncoding regions of the chloroplast genome in the Crassulaceae and related species. Curr. Genet. 25, 558 566.
    • (1994) Curr. Genet. , vol.25 , pp. 558-566
    • Van Ham, H.J.1    Hart, H.2    Mes, H.M.3    Sandbrink, J.M.4
  • 23
    • 0026562079 scopus 로고
    • The number of replications needed for accurate estimation of the bootstrap p value in phylogenetic studies
    • Hedges, S.B., 1992. The number of replications needed for accurate estimation of the bootstrap p value in phylogenetic studies. Mol. Biol. Evol. 9, 366 369.
    • (1992) Mol. Biol. Evol. , vol.9 , pp. 366-369
    • Hedges, S.B.1
  • 24
    • 0000084234 scopus 로고
    • A framework for the quantitative study of evolutionary trees
    • Hendy, M.D., Penny, D., 1989. A framework for the quantitative study of evolutionary trees. Syst. Zool. 38, 297 309.
    • (1989) Syst. Zool. , vol.38 , pp. 297-309
    • Hendy, M.D.1    Penny, D.2
  • 25
    • 0029834661 scopus 로고    scopus 로고
    • Inferring complex phylogenies
    • Hillis, D.M., 1996. Inferring complex phylogenies. Nature 383, 130 131.
    • (1996) Nature , vol.383 , pp. 130-131
    • Hillis, D.M.1
  • 26
    • 0032023889 scopus 로고    scopus 로고
    • Taxonomic sampling, phylogenetic accuracy, and investigator bias
    • Hillis, D.M., 1998. Taxonomic sampling, phylogenetic accuracy, and investigator bias. Syst. Biol. 47, 3 8.
    • (1998) Syst. Biol. , vol.47 , pp. 3-8
    • Hillis, D.M.1
  • 28
    • 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.
    • (2001) Bioinformatics , vol.17 , pp. 754-755
    • Huelsenbeck, J.P.1    Ronquist, F.2
  • 29
    • 0242582442 scopus 로고    scopus 로고
    • Molecular evolution of insertions and deletions in the chloroplast genome of Silene
    • Ingvarsson, P.K., Ribstein, S., Taylor, D.R., 2003. Molecular evolution of insertions and deletions in the chloroplast genome of Silene. Mol. Biol. Evol. 20, 1737 1740.
    • (2003) Mol. Biol. Evol. , vol.20 , pp. 1737-1740
    • Ingvarsson, P.K.1    Ribstein, S.2    Taylor, D.R.3
  • 30
    • 0141721403 scopus 로고    scopus 로고
    • Indels in protein-coding sequences of Euarchontoglires constrain the rooting of the eutherian tree
    • de Jong, W.W., van Dijk, M.A.M., Poux, C., Kappé, G., van Rheede, T., Madsen, O., 2003. Indels in protein-coding sequences of Euarchontoglires constrain the rooting of the eutherian tree. Mol. Phylogenet. Evol. 28, 328 340.
    • (2003) Mol. Phylogenet. Evol. , vol.28 , pp. 328-340
    • De Jong, W.W.1    Van Dijk, A.M.2    Poux, C.3    Kappé, G.4    Van Rheede, T.5    Madsen, O.6
  • 31
    • 0032773940 scopus 로고    scopus 로고
    • Homoplasy increases phylogenetic structure
    • Källersjö, M., Albert, V.A., Farris, J.S., 1999. Homoplasy increases phylogenetic structure. Cladistics 15, 91 93.
    • (1999) Cladistics , vol.15 , pp. 91-93
    • Källersjö, M.1    Albert, V.A.2    Farris, J.S.3
  • 32
    • 0037100671 scopus 로고    scopus 로고
    • MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform
    • Katoh, K., Misawa, K., Kuma, K., Miyata, T., 2002. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30, 3059 3066.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 3059-3066
    • Katoh, K.1    Misawa, K.2    Kuma, K.3    Miyata, T.4
  • 33
    • 13744252890 scopus 로고    scopus 로고
    • MAFFT, Version 5: Improvement in accuracy of multiple sequence alignment
    • Katoh, K., Kuma, K., Toh, H., Miyata, T., 2005. MAFFT, Version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 33, 511 518.
    • (2005) Nucleic Acids Res. , vol.33 , pp. 511-518
    • Katoh, K.1    Kuma, K.2    Toh, H.3    Miyata, T.4
  • 34
    • 0037228571 scopus 로고    scopus 로고
    • Evolution and phylogenetic utility of alignment gaps within intron sequences of three nuclear genes in bumble bees (Bombus)
    • Kawakita, A., Sota, T., Ascher, J.S., Ito, M., Tanaka, H., Kato, M., 2003. Evolution and phylogenetic utility of alignment gaps within intron sequences of three nuclear genes in bumble bees (Bombus). Mol. Biol. Evol. 20, 87 92.
    • (2003) Mol. Biol. Evol. , vol.20 , pp. 87-92
    • Kawakita, A.1    Sota, T.2    Ascher, J.S.3    Ito, M.4    Tanaka, H.5    Kato, M.6
  • 35
    • 0035845578 scopus 로고    scopus 로고
    • Lateral transfer at the gene and subgenic levels in the evolution of eukaryotic enolase
    • Keeling, P.J., Palmer, J.D., 2001. Lateral transfer at the gene and subgenic levels in the evolution of eukaryotic enolase. Proc. Natl Acad. Sci. USA 98, 10745 10750.
    • (2001) Proc. Natl Acad. Sci. USA , vol.98 , pp. 10745-10750
    • Keeling, P.J.1    Palmer, J.D.2
  • 36
    • 84959806898 scopus 로고
    • A concern for evidence and a phylogenetic hypothesis for relationships among Epicrates (Boidae, Serpentes)
    • Kluge, A.G., 1989. A concern for evidence and a phylogenetic hypothesis for relationships among Epicrates (Boidae, Serpentes). Syst. Zool. 38, 7 25.
    • (1989) Syst. Zool. , vol.38 , pp. 7-25
    • Kluge, A.G.1
  • 37
    • 0025905252 scopus 로고
    • The order of sequence alignment can bias the selection of tree topology
    • Lake, J.A., 1991. The order of sequence alignment can bias the selection of tree topology. Mol. Biol. Evol. 8, 378 385.
    • (1991) Mol. Biol. Evol. , vol.8 , pp. 378-385
    • Lake, J.A.1
  • 38
    • 0037010180 scopus 로고    scopus 로고
    • Quality assessment of multiple alignment programs
    • Lassmann, T., Sonnhammer, E.L.L., 2002. Quality assessment of multiple alignment programs. FEBS Lett. 529, 126 130.
    • (2002) FEBS Lett. , vol.529 , pp. 126-130
    • Lassmann, T.1    Sonnhammer, L.L.2
  • 39
    • 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. Scr. 34, 101 117.
    • (2005) Zool. Scr. , vol.34 , pp. 101-117
    • Lecointre, G.1    Deleporte, P.2
  • 41
    • 0031156914 scopus 로고    scopus 로고
    • Phylogenetic relationships of the liverworts (Hepaticeae), a basal embryophyte lineage, inferred from nucleotide sequence data of the chloroplast gene rbcL
    • Lewis, L.A., Mishler, B.D., Vilgalys, R., 1997. Phylogenetic relationships of the liverworts (Hepaticeae), a basal embryophyte lineage, inferred from nucleotide sequence data of the chloroplast gene rbcL. Mol. Phylogenet. Evol. 7, 377 393.
    • (1997) Mol. Phylogenet. Evol. , vol.7 , pp. 377-393
    • Lewis, L.A.1    Mishler, B.D.2    Vilgalys, R.3
  • 42
    • 2342555111 scopus 로고    scopus 로고
    • Phylogenetic analysis of the plant endo-B-1,4-glucanase gene family
    • Libertini, E., Li, Y., McQueen-Mason, S.J., 2004. Phylogenetic analysis of the plant endo-B-1,4-glucanase gene family. J. Mol. Evol. 58, 506 515.
    • (2004) J. Mol. Evol. , vol.58 , pp. 506-515
    • Libertini, E.1    Li, Y.2    McQueen-Mason, S.J.3
  • 43
    • 84993911710 scopus 로고
    • Multi-residue gaps, a class of molecular characters with exceptional reliability for phylogenetic analyses
    • Lloyd, D.G., Calder, V.L., 1991. Multi-residue gaps, a class of molecular characters with exceptional reliability for phylogenetic analyses. J. Evol. Biol. 4, 9 21.
    • (1991) J. Evol. Biol. , vol.4 , pp. 9-21
    • Lloyd, D.G.1    Calder, V.L.2
  • 44
    • 0026681831 scopus 로고
    • Substitutional bias confounds inference of cyanelle origins from sequence data
    • Lockhart, P.J., Howe, C.J., Bryant, D.A., Beanland, T.J., Larkum, A.W.D., 1992a. Substitutional bias confounds inference of cyanelle origins from sequence data. J. Mol. Evol. 34, 153 162.
    • (1992) J. Mol. Evol. , vol.34 , pp. 153-162
    • Lockhart, P.J.1    Howe, C.J.2    Bryant, D.A.3    Beanland, T.J.4    Larkum, W.D.5
  • 47
    • 0141888247 scopus 로고    scopus 로고
    • Phylogenetic relationships of the fox (forkhead) gene family in the Bilateria
    • Mazet, F., You, J.-K., Liberles, D.A., Holland, L.Z., Shimeld, S.M., 2003. Phylogenetic relationships of the fox (forkhead) gene family in the Bilateria. Gene 316, 79 89.
    • (2003) Gene , vol.316 , pp. 79-89
    • Mazet, F.1    You, J.-K.2    Liberles, D.A.3    Holland, L.Z.4    Shimeld, S.M.5
  • 48
    • 0028156627 scopus 로고
    • Shortcomings of the cytochrome b gene as a molecular marker
    • Meyer, A., 1994. Shortcomings of the cytochrome b gene as a molecular marker. Trends Ecol. Evol. 9, 278 280.
    • (1994) Trends Ecol. Evol. , vol.9 , pp. 278-280
    • Meyer, A.1
  • 49
    • 0032945593 scopus 로고    scopus 로고
    • DIALIGN 2: Improvement of the segment-to-segment approach to multiple sequence alignment
    • Morgenstern, B., 1999. DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment. Bioinformatics 15, 211 218.
    • (1999) Bioinformatics , vol.15 , pp. 211-218
    • Morgenstern, B.1
  • 50
    • 0031854952 scopus 로고    scopus 로고
    • DIALIGN: Finding local similarities by multiple sequence alignment
    • Morgenstern, B., Frech, K., Dress, A., Werner, T., 1998. DIALIGN: finding local similarities by multiple sequence alignment. Bioinformatics 14, 290 294.
    • (1998) Bioinformatics , vol.14 , pp. 290-294
    • Morgenstern, B.1    Frech, K.2    Dress, A.3    Werner, T.4
  • 51
    • 0030934592 scopus 로고    scopus 로고
    • Effects of nucleotide sequence alignment on phylogeny estimation: A case study of 18S rDNAs of Apicomplexa
    • Morrison, D.A., Ellis, J.T., 1997. Effects of nucleotide sequence alignment on phylogeny estimation: a case study of 18S rDNAs of Apicomplexa. Mol. Biol. Evol. 14, 428 441.
    • (1997) Mol. Biol. Evol. , vol.14 , pp. 428-441
    • Morrison, D.A.1    Ellis, J.T.2
  • 52
    • 22944482184 scopus 로고    scopus 로고
    • Seqstate - Primer design and sequence statistics for phylogenetic DNA data sets
    • Müller, K., 2005. Seqstate - primer design and sequence statistics for phylogenetic DNA data sets. Appl. Bioinform. 4, 65 69.
    • (2005) Appl. Bioinform. , vol.4 , pp. 65-69
    • Müller, K.1
  • 53
    • 33244488048 scopus 로고    scopus 로고
    • Incorporating information from length-mutational events into phylogenetic analysis
    • Müller, K., 2006. Incorporating information from length-mutational events into phylogenetic analysis. Mol. Phylogenet. Evol. 38, 667 676.
    • (2006) Mol. Phylogenet. Evol. , vol.38 , pp. 667-676
    • Müller, K.1
  • 54
    • 0042592785 scopus 로고    scopus 로고
    • On simultaneous analysis
    • Nixon, K.C., Carpenter, J.M., 1996. On simultaneous analysis. Cladistics 12, 221 242.
    • (1996) Cladistics , vol.12 , pp. 221-242
    • Nixon, K.C.1    Carpenter, J.M.2
  • 55
    • 0002272008 scopus 로고
    • Extinction and the origin of species
    • In: Wheeler, Q.D., Novacek, M. (Eds. Columbia University Press, New York, pp.
    • Nixon, K.C., Wheeler, Q.D., 1991. Extinction and the origin of species. In : Wheeler, Q.D., Novacek, M. (Eds Extinction and Phylogeny. Columbia University Press, New York, pp. 119 143.
    • (1991) Extinction and Phylogeny. , pp. 119-143
    • Nixon, K.C.1    Wheeler, Q.D.2
  • 56
    • 0034623005 scopus 로고    scopus 로고
    • T-Coffee: A novel method for fast and accurate multiple sequence alignment
    • Notredame, C., Higgins, D.G., Heringa, J., 2000. T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 302, 205 217.
    • (2000) J. Mol. Biol. , vol.302 , pp. 205-217
    • Notredame, C.1    Higgins, D.G.2    Heringa, J.3
  • 57
    • 0029907143 scopus 로고    scopus 로고
    • A critical study of homoplasy in molecular data with the use of a morphologically based cladogram, and its consequences for character weighting
    • Philippe, H., Lecointre, G., Lê, H.L.V., Le Guyader, H., 1996. A critical study of homoplasy in molecular data with the use of a morphologically based cladogram, and its consequences for character weighting. Mol. Biol. Evol. 13, 1174 1186.
    • (1996) Mol. Biol. Evol. , vol.13 , pp. 1174-1186
    • Philippe, H.1    Lecointre, G.2    Lê, L.V.3    Le Guyader, H.4
  • 59
    • 33645107555 scopus 로고    scopus 로고
    • Size, frequency, and phylogenetic signal of multiple-residue indels in sequence alignment of introns
    • Pons, J., Vogler, A.P., 2006. Size, frequency, and phylogenetic signal of multiple-residue indels in sequence alignment of introns. Cladistics 22, 144 156.
    • (2006) Cladistics , vol.22 , pp. 144-156
    • Pons, J.1    Vogler, A.P.2
  • 60
    • 0037143610 scopus 로고    scopus 로고
    • Phylogenetic analysis of the Wnt gene family: Insights from Lophotrochozoan members
    • Prud'homme, B., Lartillot, N., Balavoine, G., Adoutte, A., Vervoort, M., 2002. Phylogenetic analysis of the Wnt gene family: insights from Lophotrochozoan members. Curr. Biol. 12, 1395 1400.
    • (2002) Curr. Biol. , vol.12 , pp. 1395-1400
    • Prud'Homme, B.1    Lartillot, N.2    Balavoine, G.3    Adoutte, A.4    Vervoort, M.5
  • 61
    • 33645774434 scopus 로고    scopus 로고
    • Molecular motors in plant cells
    • In: Meyer, R. (Ed.), Wiley. Weinheim, pp.
    • Reddy, A.S.N., 2005. Molecular motors in plant cells. In : Meyer, R. (Ed.), Encyclopedia of Molecular Cell Biology and Molecular Medicine, Vol. 8. Wiley-VCH Publishers, Weinheim, pp. 461 494.
    • (2005) Encyclopedia of Molecular Cell Biology and Molecular Medicine , vol.8 , pp. 461-494
    • Reddy, S.N.1
  • 62
    • 22844450838 scopus 로고    scopus 로고
    • Joint Bayesian estimation of alignment and phylogeny
    • Redelings, B.D., Suchard, M.A., 2005. Joint Bayesian estimation of alignment and phylogeny. Syst. Biol. 54, 401 418.
    • (2005) Syst. Biol. , vol.54 , pp. 401-418
    • Redelings, B.D.1    Suchard, M.A.2
  • 63
    • 24144503755 scopus 로고    scopus 로고
    • Myosin domain evolution and the primary divergence of eukaryotes
    • Richards, T.A., Cavalier-Smith, T., 2005. Myosin domain evolution and the primary divergence of eukaryotes. Nature 436, 1113 1118.
    • (2005) Nature , vol.436 , pp. 1113-1118
    • Richards, T.A.1    Cavalier-Smith, T.2
  • 64
    • 33645757529 scopus 로고    scopus 로고
    • Comprehensive comparative analysis of kinesins in photosynthetic eukaryotes
    • Richardson, D., Simmons, M.P., Reddy, A.S.N., 2006. Comprehensive comparative analysis of kinesins in photosynthetic eukaryotes. BMC Genomics 7, 18.
    • (2006) BMC Genomics , vol.7 , pp. 18
    • Richardson, D.1    Simmons, M.P.2    Reddy, S.N.3
  • 65
    • 0019424782 scopus 로고
    • Comparison of phylogenetic trees
    • Robinson, D.F., Foulds, L.R., 1981. Comparison of phylogenetic trees. Math. Biosci. 53, 131 147.
    • (1981) Math. Biosci. , vol.53 , pp. 131-147
    • Robinson, D.F.1    Foulds, L.R.2
  • 66
    • 0033793019 scopus 로고    scopus 로고
    • Rare genomic changes as a tool for phylogenetics
    • Rokas, A., Holland, P.W.H., 2000. Rare genomic changes as a tool for phylogenetics. Trends Ecol. Evol. 15, 454 459.
    • (2000) Trends Ecol. Evol. , vol.15 , pp. 454-459
    • Rokas, A.1    Holland, W.H.2
  • 68
    • 0000215283 scopus 로고    scopus 로고
    • Success of parsimony in the four-taxon case: Long-branch repulsion by likelihood in the Farris Zone
    • Siddall, M.E., 1998. Success of parsimony in the four-taxon case: long-branch repulsion by likelihood in the Farris Zone. Cladistics 14, 209 220.
    • (1998) Cladistics , vol.14 , pp. 209-220
    • Siddall, M.E.1
  • 69
    • 2442507933 scopus 로고    scopus 로고
    • Independence of alignment and tree search
    • Simmons, M.P., 2004. Independence of alignment and tree search. Mol. Phylogenet. Evol. 31, 874 879.
    • (2004) Mol. Phylogenet. Evol. , vol.31 , pp. 874-879
    • Simmons, M.P.1
  • 70
    • 0037355122 scopus 로고    scopus 로고
    • The effects of increasing genetic distance on alignment of, and tree construction from, rDNA internal transcribed spacer sequences
    • Simmons, M.P., Freudenstein, J.V., 2003. The effects of increasing genetic distance on alignment of, and tree construction from, rDNA internal transcribed spacer sequences. Mol. Phylogenet. Evol. 26, 444 451.
    • (2003) Mol. Phylogenet. Evol. , vol.26 , pp. 444-451
    • Simmons, M.P.1    Freudenstein, J.V.2
  • 71
    • 1642546638 scopus 로고    scopus 로고
    • Efficiently resolving the basal clades of a phylogenetic tree using Bayesian and parsimony approaches: A case study using mitogenomic data from 100 higher teleost fishes
    • Simmons, M.P., Miya, M., 2004. Efficiently resolving the basal clades of a phylogenetic tree using Bayesian and parsimony approaches: a case study using mitogenomic data from 100 higher teleost fishes. Mol. Phylogenet. Evol. 31, 351 362.
    • (2004) Mol. Phylogenet. Evol. , vol.31 , pp. 351-362
    • Simmons, M.P.1    Miya, M.2
  • 72
    • 0034350427 scopus 로고    scopus 로고
    • Gaps as characters in sequence-based phylogenetic analyses
    • Simmons, M.P., Ochoterena, H., 2000. Gaps as characters in sequence-based phylogenetic analyses. Syst. Biol. 49, 369 381.
    • (2000) Syst. Biol. , vol.49 , pp. 369-381
    • Simmons, M.P.1    Ochoterena, H.2
  • 73
    • 33745034045 scopus 로고    scopus 로고
    • Quantification of the success of phylogenetic inference in simulations
    • Simmons, M.P., Webb, C.T., 2006. Quantification of the success of phylogenetic inference in simulations. Cladistics 22, 249 305.
    • (2006) Cladistics , vol.22 , pp. 249-305
    • Simmons, M.P.1    Webb, C.T.2
  • 74
    • 0035527375 scopus 로고    scopus 로고
    • Incorporation, relative homoplasy, and effect of gap characters in sequence-based phylogenetic analyses
    • Simmons, M.P., Ochoterena, H., Carr, T.G., 2001. Incorporation, relative homoplasy, and effect of gap characters in sequence-based phylogenetic analyses. Syst. Biol. 50, 454 462.
    • (2001) Syst. Biol. , vol.50 , pp. 454-462
    • Simmons, M.P.1    Ochoterena, H.2    Carr, T.G.3
  • 75
    • 1242352069 scopus 로고    scopus 로고
    • How meaningful are Bayesian posterior probabilities?
    • Simmons, M.P., Pickett, K.M., Miya, M., 2004. How meaningful are Bayesian posterior probabilities? Mol. Biol. Evol. 21, 188 199.
    • (2004) Mol. Biol. Evol. , vol.21 , pp. 188-199
    • Simmons, M.P.1    Pickett, K.M.2    Miya, M.3
  • 76
    • 34447280568 scopus 로고    scopus 로고
    • The relative performance of indel-coding methods in simulations
    • Simmons, M.P., Müller, K., Norton, A.P., 2007. The relative performance of indel-coding methods in simulations. Mol. Phylogenet. Evol. 44, 724 740.
    • (2007) Mol. Phylogenet. Evol. , vol.44 , pp. 724-740
    • Simmons, M.P.1    Müller, K.2    Norton, A.P.3
  • 77
    • 0345676554 scopus 로고    scopus 로고
    • Multiple sequence alignment with the divide-and-conquer method
    • Stoye, J., 1998. Multiple sequence alignment with the divide-and-conquer method. Gene 211, GC45 GC56.
    • (1998) Gene , vol.211
    • Stoye, J.1
  • 79
    • 0037058983 scopus 로고    scopus 로고
    • Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics
    • Suzuki, Y., Glazko, G.V., Nei, M., 2002. Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics. Proc. Natl Acad. Sci. USA 99, 16138 16143.
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 16138-16143
    • Suzuki, Y.1    Glazko, G.V.2    Nei, M.3
  • 81
    • 0035527406 scopus 로고    scopus 로고
    • Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods
    • Swofford, D.L., Waddell, P.J., Huelsenbeck, J.P., Foster, P.G., Lewis, P.O., Rogers, J.S., 2001. Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods. Syst. Biol. 50, 525 539.
    • (2001) Syst. Biol. , vol.50 , 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
  • 82
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson, J.D., Higgins, D.G., Gibson, T.J., 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673 4680.
    • (1994) Nucleic Acids Res. , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 83
    • 0031574072 scopus 로고    scopus 로고
    • The CLUSTAL_X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools
    • Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F., Higgins, D.G., 1997. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25, 4876 4882.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 4876-4882
    • Thompson, J.D.1    Gibson, T.J.2    Plewniak, F.3    Jeanmougin, F.4    Higgins, D.G.5
  • 84
    • 0033168097 scopus 로고    scopus 로고
    • A comprehensive comparison of multiple sequence alignment programs
    • Thompson, J.D., Plewniak, F., Poch, O., 1999. A comprehensive comparison of multiple sequence alignment programs. Nucleic Acids Res. 27, 2682 2690.
    • (1999) Nucleic Acids Res. , vol.27 , pp. 2682-2690
    • Thompson, J.D.1    Plewniak, F.2    Poch, O.3
  • 85
    • 0026458222 scopus 로고
    • Freeing phylogenies from artifacts of alignment
    • Thorne, J.L., Kishino, H., 1992. Freeing phylogenies from artifacts of alignment. Mol. Biol. Evol. 9, 1148 1162.
    • (1992) Mol. Biol. Evol. , vol.9 , pp. 1148-1162
    • Thorne, J.L.1    Kishino, H.2
  • 86
    • 0026079507 scopus 로고
    • An evolutionary model for maximum likelihood alignment of DNA sequences
    • Thorne, J.L., Kishino, H., Felsenstein, J., 1991. An evolutionary model for maximum likelihood alignment of DNA sequences. J. Mol. Evol. 33, 114 124.
    • (1991) J. Mol. Evol. , vol.33 , pp. 114-124
    • Thorne, J.L.1    Kishino, H.2    Felsenstein, J.3
  • 87
    • 0029884395 scopus 로고    scopus 로고
    • A general method for fast multiple sequence alignment
    • Tönges, U., Perry, S.W., Stoye, J., Dress, A.W.M., 1996. A general method for fast multiple sequence alignment. Gene 172, GC33 GC41.
    • (1996) Gene , vol.172
    • Tönges, U.1    Perry, S.W.2    Stoye, J.3    Dress, W.M.4
  • 88
    • 0031149251 scopus 로고    scopus 로고
    • Links between maximum likelihood and maximum parsimony under a simple model of site substitution
    • Tuffley, C., Steel, M., 1997. Links between maximum likelihood and maximum parsimony under a simple model of site substitution. B. Math. Biol. 59, 581 607.
    • (1997) B. Math. Biol. , vol.59 , pp. 581-607
    • Tuffley, C.1    Steel, M.2
  • 89
    • 3042613056 scopus 로고    scopus 로고
    • Align-m - A new algorithm for multiple alignment of highly divergent sequences
    • Van Walle, I., Lasters, I., Wyns, L., 2004. Align-m - a new algorithm for multiple alignment of highly divergent sequences. Bioinformatics 20, 1428 1435.
    • (2004) Bioinformatics , vol.20 , pp. 1428-1435
    • Van Walle, I.1    Lasters, I.2    Wyns, L.3
  • 91
    • 0028878618 scopus 로고
    • Sequence alignment, parameter sensitivity, and the phylogenetic analysis of molecular data
    • Wheeler, W.C., 1995. Sequence alignment, parameter sensitivity, and the phylogenetic analysis of molecular data. Syst. Biol. 44, 321 331.
    • (1995) Syst. Biol. , vol.44 , pp. 321-331
    • Wheeler, W.C.1
  • 92
    • 0001857390 scopus 로고    scopus 로고
    • Optimization alignment: The end of multiple sequence alignment in phylogenetics?
    • Wheeler, W., 1996. Optimization alignment: the end of multiple sequence alignment in phylogenetics? Cladistics 12, 1 10.
    • (1996) Cladistics , vol.12 , pp. 1-10
    • Wheeler, W.1
  • 93
    • 13444251103 scopus 로고    scopus 로고
    • Version 3.0.11. New York, Distributed by the authors.
    • Wheeler, W., Gladstein, D., De Laet, J., 2003. POY, Version 3.0.11. New York, Distributed by the authors.
    • (2003) POY
    • Wheeler, W.1    Gladstein, D.2    De Laet, J.3
  • 94
    • 0032225748 scopus 로고    scopus 로고
    • Does adding characters with missing data increase or decrease phylogenetic accuracy?
    • Wiens, J.J., 1998. Does adding characters with missing data increase or decrease phylogenetic accuracy? Syst. Biol. 47, 625 640.
    • (1998) Syst. Biol. , vol.47 , pp. 625-640
    • Wiens, J.J.1
  • 95
    • 0042905752 scopus 로고    scopus 로고
    • Missing data, incomplete taxa, and phylogenetic accuracy
    • Wiens, J.J., 2003. Missing data, incomplete taxa, and phylogenetic accuracy. Syst. Biol. 52, 528 538.
    • (2003) Syst. Biol. , vol.52 , pp. 528-538
    • Wiens, J.J.1
  • 96
    • 0032028624 scopus 로고    scopus 로고
    • On the best evolutionary rate for phylogenetic analysis
    • Yang, Z., 1998. On the best evolutionary rate for phylogenetic analysis. Syst. Biol. 47, 125 133.
    • (1998) Syst. Biol. , vol.47 , pp. 125-133
    • Yang, Z.1
  • 97
    • 0030749810 scopus 로고    scopus 로고
    • Bayesian phylogenetic inference using DNA sequences: A Markov Chain Monte Carlo method
    • Yang, Z., Rannala, B., 1997. Bayesian phylogenetic inference using DNA sequences: a Markov Chain Monte Carlo method. Mol. Biol. Evol. 14, 717 724.
    • (1997) Mol. Biol. Evol. , vol.14 , pp. 717-724
    • Yang, Z.1    Rannala, B.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.