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Volumn 4, Issue , 2003, Pages

GapCoder automates the use of indel characters in phylogenetic analysis

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ANALYTIC METHOD; ARTICLE; AUTOMATION; CODING AND CLASSIFICATION; COMPUTER PROGRAM; CONTROLLED STUDY; GENE SEQUENCE; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; BIOLOGY; CLASSIFICATION; DNA SEQUENCE; GENE DELETION; GENE EXPRESSION REGULATION; GENETIC DATABASE; GENETICS; METHODOLOGY;

EID: 0642309746     PISSN: 14712105     EISSN: None     Source Type: Journal    
DOI: 10.1186/1471-2105-4-6     Document Type: Article
Times cited : (382)

References (21)
  • 1
    • 0027501821 scopus 로고
    • Taxonomic congruence versus total evidence, and amniote phylogeny inferred from fossils, molecules, and morphology
    • Eernisse DJ and Kluge AG Taxonomic congruence versus total evidence, and amniote phylogeny inferred from fossils, molecules, and morphology. Mol Biol Evol 1993, 10:1170-1195
    • (1993) Mol. Biol. Evol. , vol.10 , pp. 1170-1195
    • Eernisse, D.J.1    Kluge, A.G.2
  • 2
    • 0028226508 scopus 로고
    • Evolution and phylogenetic information content of the ITS-1 region in the tiger beetle Cicindela dorsalis
    • Vogler AP and DeSalle R Evolution and phylogenetic information content of the ITS-1 region in the tiger beetle Cicindela dorsalis. Mol Biol Evol 1994, 11:393-405
    • (1994) Mol. Biol. Evol. , vol.11 , pp. 393-405
    • Vogler, A.P.1    DeSalle, R.2
  • 3
    • 0000738704 scopus 로고    scopus 로고
    • Phylogenetic relationships of the creek chubs and the spine-fins: An enigmatic group of North American cyprinid fishes (Actinopterygii: Cyprinidae)
    • Simmons AM and Mayden RL Phylogenetic relationships of the creek chubs and the spine-fins: An enigmatic group of North American cyprinid fishes (Actinopterygii: Cyprinidae). Cladistics 1997, 13:187-206
    • (1997) Cladistics , vol.13 , pp. 187-206
    • Simmons, A.M.1    Mayden, R.L.2
  • 4
    • 0034789422 scopus 로고    scopus 로고
    • Analysis of mitochondrial nad1b-c intron sequences in Orchidaceae: Utility and coding of length-change characters
    • Freudenstein JV and Chase MW Analysis of mitochondrial nad1b-c intron sequences in Orchidaceae: Utility and coding of length-change characters. Syst Bot 2001, 26:643-657
    • (2001) Syst. Bot. , vol.26 , pp. 643-657
    • Freudenstein, J.V.1    Chase, M.W.2
  • 6
    • 84993911710 scopus 로고
    • Multi-residue gaps, a class of molecular characters with exceptional reliability for phylogenetic analyses
    • Lloyd DG and Calder VL Multi-residue gaps, a class of molecular characters with exceptional reliability for phylogenetic analyses. J Evol Biol 1991, 4:9-21
    • (1991) J. Evol. Biol. , vol.4 , pp. 9-21
    • Lloyd, D.G.1    Calder, V.L.2
  • 7
    • 0028346242 scopus 로고
    • Molecular evolution of noncoding regions of the chloroplast genome in the Crassulaceae and related species
    • Van Ham RCHJ, Hart H, Mes THM and Sandbrink JM Molecular evolution of noncoding regions of the chloroplast genome in the Crassulaceae and related species. Curr Genet 1994, 25:558-566
    • (1994) Curr. Genet. , vol.25 , pp. 558-566
    • Van Ham, R.C.H.J.1    Hart, H.2    Mes, T.H.M.3    Sandbrink, J.M.4
  • 8
    • 0000890115 scopus 로고
    • Phylogenetic inference in Saxifragaceae sensu stricto and Gilia (Polemoniaceae) using mat K sequences
    • Johnson LA and Soltis DE Phylogenetic inference in Saxifragaceae sensu stricto and Gilia (Polemoniaceae) using mat K sequences. Ann Mo Bot Gard 1995, 82:149-175
    • (1995) Ann. Mo. Bot. Gard. , vol.82 , pp. 149-175
    • Johnson, L.A.1    Soltis, D.E.2
  • 9
    • 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 BG and Markos S Phylogenetic utility of the external transcribed spacer (ETS) of 18S-26S rDNA: Congruence of ETS and ITS trees of Calycadenia (Compositae). Mol Phylogenet Evol 1998, 10:449-463
    • (1998) Mol. Phylogenet. Evol. , vol.10 , pp. 449-463
    • Baldwin, B.G.1    Markos, S.2
  • 10
    • 0031970356 scopus 로고    scopus 로고
    • Phylogeny of Cobaea (Polemoniaceae) based on sequence data from the ITS region of nuclear ribosomal DNA
    • Prather LA and Jansen RK Phylogeny of Cobaea (Polemoniaceae) based on sequence data from the ITS region of nuclear ribosomal DNA. Syst Bot 1998, 23:57-72
    • (1998) Syst. Bot. , vol.23 , pp. 57-72
    • Prather, L.A.1    Jansen, R.K.2
  • 11
    • 0035527375 scopus 로고    scopus 로고
    • Incorporation, relative homoplasy, and effect of gap characters in sequence-based phylogenetic analysis
    • Simmons MP, Ochoterena H and Carr TG Incorporation, relative homoplasy, and effect of gap characters in sequence-based phylogenetic analysis. Syst Biol 2001, 50:454-462
    • (2001) Syst. Biol. , vol.50 , pp. 454-462
    • Simmons, M.P.1    Ochoterena, H.2    Carr, T.G.3
  • 12
    • 0028087774 scopus 로고
    • MALIGN: A multiple sequence alignment program
    • Wheeler WC and Gladstein DS MALIGN: A multiple sequence alignment program. J Hered 1994, 85:417-418
    • (1994) J. Hered. , vol.85 , pp. 417-418
    • Wheeler, W.C.1    Gladstein, D.S.2
  • 14
    • 0026566796 scopus 로고
    • Analysis of insertions/deletions in protein structures
    • Pascarella S and Argos P Analysis of insertions/deletions in protein structures. J Mol Biol 1992, 224:461-471
    • (1992) J. Mol. Biol. , vol.224 , pp. 461-471
    • Pascarella, S.1    Argos, P.2
  • 15
    • 0028943946 scopus 로고
    • The size distribution of insertions and deletions in human and rodent pseudogenes suggests the logarithmic gap penalty for sequence alignment
    • Gu X and Li W-H The size distribution of insertions and deletions in human and rodent pseudogenes suggests the logarithmic gap penalty for sequence alignment. J Mol Evol 1995, 40:464-473
    • (1995) J. Mol. Evol. , vol.40 , pp. 464-473
    • Gu, X.1    Li, W.-H.2
  • 16
    • 0034350427 scopus 로고    scopus 로고
    • Gaps as characters in sequence-based phylogenetic analyses
    • Simmons MP and Ochoterena H Gaps as characters in sequence-based phylogenetic analyses. Syst Biol 2000, 49:369-381
    • (2000) Syst. Biol. , vol.49 , pp. 369-381
    • Simmons, M.P.1    Ochoterena, H.2
  • 17
    • 0001857390 scopus 로고    scopus 로고
    • Optimization alignment: The end of multiple alignment in phylogenetics?
    • Wheeler WC Optimization alignment:the end of multiple alignment in phylogenetics? Cladistics 1996, 12:1-9
    • (1996) Cladistics , vol.12 , pp. 1-9
    • Wheeler, W.C.1
  • 18
    • 0028093739 scopus 로고
    • A phylogenetic analysis of Epilobium (Onagraceae) based on nuclear ribosomal DNA sequences
    • Baum DA, Sytsma KJ and Hoch PC A phylogenetic analysis of Epilobium (Onagraceae) based on nuclear ribosomal DNA sequences. Syst Bot 1994, 19:363-388
    • (1994) Syst. Bot. , vol.19 , pp. 363-388
    • Baum, D.A.1    Sytsma, K.J.2    Hoch, P.C.3
  • 19
    • 0033387629 scopus 로고    scopus 로고
    • Steiner KE and dePamphilis CW The evolution of parasitism in Scrophulariaceae/Orobanchaceae: Plastid gene sequences refute an evolutionary transition series
    • Young ND, Steiner KE and dePamphilis CW The evolution of parasitism in Scrophulariaceae/Orobanchaceae: plastid gene sequences refute an evolutionary transition series. Ann Missouri Bot Gard 1999, 86:876-893
    • (1999) Ann. Missouri Bot. Gard. , vol.86 , pp. 876-893
    • Young, N.D.1
  • 20
    • 0034351388 scopus 로고    scopus 로고
    • Integrating ambiguously aligned regions of DNA sequences in phylogenetic analyses without violating positional homology
    • Lutzoni F, Wagner P, Reeb V and Zoller S Integrating ambiguously aligned regions of DNA sequences in phylogenetic analyses without violating positional homology. Syst Biol 2000,49:628-651
    • (2000) Syst. Biol. , vol.49 , pp. 628-651
    • Lutzoni, F.1    Wagner, P.2    Reeb, V.3    Zoller, S.4
  • 21
    • 0004248459 scopus 로고    scopus 로고
    • PAUP*. Phylogenetic analysis using parsimony (* and other methods)
    • Version 4. Sinauer Associates, Sunderland, Massachussetts
    • Swofford DL PAUP*. Phylogenetic analysis using parsimony (* and other methods). Version 4. Sinauer Associates, Sunderland, Massachussetts 1998.
    • (1998)
    • Swofford, D.L.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.