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Volumn 7, Issue 7, 2012, Pages

Analyzing multi-locus plant barcoding datasets with a composition vector method based on adjustable weighted distance

Author keywords

[No Author keywords available]

Indexed keywords

PLANT DNA;

EID: 84864402287     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0042154     Document Type: Article
Times cited : (8)

References (33)
  • 2
    • 0042531561 scopus 로고    scopus 로고
    • Barcoding animal life: cytochrome c oxidase subunit I divergences among closely related species
    • Hebert PDN, Ratnasingham S, de Waard JR, ((2003)) Barcoding animal life: cytochrome c oxidase subunit I divergences among closely related species. Proc R Soc B 270 (S1): 96--99.
    • (2003) Proc R Soc B , vol.270 , Issue.S1 , pp. 96-99
    • Hebert, P.D.N.1    Ratnasingham, S.2    de Waard, J.R.3
  • 3
    • 6944255373 scopus 로고    scopus 로고
    • Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator
    • Hebert PDN, Penton EH, Burns JM, Janzen DH, Hallwachs W, ((2004)) Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. Proc Natl Acad Sci USA 101:: 14812--14817.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 14812-14817
    • Hebert, P.D.N.1    Penton, E.H.2    Burns, J.M.3    Janzen, D.H.4    Hallwachs, W.5
  • 7
    • 38949205862 scopus 로고    scopus 로고
    • CO1 DNA barcoding amphibians: take the chance, meet the challenge
    • Smith MA, Poyarkov NA Jr, Hebert PDN, ((2008)) CO1 DNA barcoding amphibians: take the chance, meet the challenge. Mol Ecol Resour 8:: 235--246.
    • (2008) Mol Ecol Resour , vol.8 , pp. 235-246
    • Smith, M.A.1    Poyarkov Jr., N.A.2    Hebert, P.D.N.3
  • 8
    • 65349124174 scopus 로고    scopus 로고
    • Are plant species inherently harder to discriminate than animal species using DNA barcoding markers?
    • Fazekas AJ, Kesanakurti PR, Burgess KS, Percy DM, Graham SW, et al. ((2009)) Are plant species inherently harder to discriminate than animal species using DNA barcoding markers? Mol Ecol Resour 9 (S1): 130--139.
    • (2009) Mol Ecol Resour , vol.9 , Issue.S1 , pp. 130-139
    • Fazekas, A.J.1    Kesanakurti, P.R.2    Burgess, K.S.3    Percy, D.M.4    Graham, S.W.5
  • 10
    • 69149084832 scopus 로고    scopus 로고
    • A DNA barcode for land plants
    • CBOL Plant Working Group
    • CBOL Plant Working Group ((2009)) A DNA barcode for land plants. Proc Natl Acad Sci USA 106:: 12794--12797.
    • (2009) Proc Natl Acad Sci USA , vol.106 , pp. 12794-12797
  • 12
    • 70749129778 scopus 로고    scopus 로고
    • Rapid DNA barcoding analysis of large datasets using the composition vector method
    • Chu KH, Xu M, Li CP, ((2009)) Rapid DNA barcoding analysis of large datasets using the composition vector method. BMC Bioinformatics 10 (S14): S8.
    • (2009) BMC Bioinformatics , vol.10 , Issue.S14
    • Chu, K.H.1    Xu, M.2    Li, C.P.3
  • 13
    • 34248149943 scopus 로고    scopus 로고
    • BOLD: the barcode of life data system (www.barcodinglife.org)
    • Ratnasingham S, Hebert PDN, ((2007)) BOLD: the barcode of life data system (www.barcodinglife.org). Mol Ecol Notes 7:: 355--364.
    • (2007) Mol Ecol Notes , vol.7 , pp. 355-364
    • Ratnasingham, S.1    Hebert, P.D.N.2
  • 14
    • 42649090839 scopus 로고    scopus 로고
    • DNA barcoding in the cycadales: testing the potential of proposed barcoding markers for species identification of cycads
    • Sass C, Little DP, Stevenson DW, Specht CD, ((2007)) DNA barcoding in the cycadales: testing the potential of proposed barcoding markers for species identification of cycads. PLoS One 2:: e1154.
    • (2007) PLoS One , vol.2
    • Sass, C.1    Little, D.P.2    Stevenson, D.W.3    Specht, C.D.4
  • 15
    • 0036144960 scopus 로고    scopus 로고
    • Stretch coding and block coding: two new strategies to represent questionably aligned DNA sequences
    • Geiger DL, ((2002)) Stretch coding and block coding: two new strategies to represent questionably aligned DNA sequences. J Mol Evol 54:: 191--199.
    • (2002) J Mol Evol , vol.54 , pp. 191-199
    • Geiger, D.L.1
  • 16
    • 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--9.
    • (1996) Cladistics , vol.12 , pp. 1-9
    • Wheeler, W.1
  • 17
    • 33747888802 scopus 로고    scopus 로고
    • Ribosomal RNA as molecular barcodes: A simple correlation analysis without sequence alignment
    • Chu KH, Li CP, Qi J, ((2006)) Ribosomal RNA as molecular barcodes: A simple correlation analysis without sequence alignment. Bioinformatics 22:: 1690--1701.
    • (2006) Bioinformatics , vol.22 , pp. 1690-1701
    • Chu, K.H.1    Li, C.P.2    Qi, J.3
  • 18
    • 80051683629 scopus 로고    scopus 로고
    • DNA barcode sequence identification incorporating taxonomic hierarchy and within taxon variability
    • Little DP, ((2011)) DNA barcode sequence identification incorporating taxonomic hierarchy and within taxon variability. PLoS One 6:: e20552.
    • (2011) PLoS One , vol.6
    • Little, D.P.1
  • 19
    • 1242335920 scopus 로고    scopus 로고
    • Whole proteome prokaryote phylogeny without sequence alignment: a K-string composition approach
    • Qi J, Wang B, Hao BL, ((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.L.3
  • 20
    • 3242890106 scopus 로고    scopus 로고
    • CVTree: a phylogenetic tree reconstruction tool based on whole genomes
    • Qi J, Luo H, Hao B, ((2004)) CVTree: a phylogenetic tree reconstruction tool based on whole genomes. Nucl Acids Res 32:: W1--W3.
    • (2004) Nucl Acids Res , vol.32
    • Qi, J.1    Luo, H.2    Hao, B.3
  • 21
    • 0035898770 scopus 로고    scopus 로고
    • Distance, correlation and mutual information among portraits of organisms based on complete genomes
    • Yu ZG, Jiang P, ((2001)) Distance, correlation and mutual information among portraits of organisms based on complete genomes. Phys Lett A 286:: 34--46.
    • (2001) Phys Lett A , vol.286 , pp. 34-46
    • Yu, Z.G.1    Jiang, P.2
  • 22
    • 19944366976 scopus 로고    scopus 로고
    • Phylogeny of prokaryotes and chloroplasts revealed by a simple composition approach on all protein sequences from whole genome without sequence alignment
    • Yu ZG, Zhou LQ, Anh VV, Chu KH, Long SC, et al. ((2005)) Phylogeny of prokaryotes and chloroplasts revealed by a simple composition approach on all protein sequences from whole genome without sequence alignment. J Mol Evol 60:: 538--545.
    • (2005) J Mol Evol , vol.60 , pp. 538-545
    • Yu, Z.G.1    Zhou, L.Q.2    Anh, V.V.3    Chu, K.H.4    Long, S.C.5
  • 23
    • 77950895944 scopus 로고    scopus 로고
    • Proper distance matrices for phylogenetic analysis using complete genomes without sequence alignment
    • Yu ZG, Zhan XW, Han GS, Wang RW, Anh V, et al. ((2010)) Proper distance matrices for phylogenetic analysis using complete genomes without sequence alignment. Int J Mol Sci 11:: 1141--1154.
    • (2010) Int J Mol Sci , vol.11 , pp. 1141-1154
    • Yu, Z.G.1    Zhan, X.W.2    Han, G.S.3    Wang, R.W.4    Anh, V.5
  • 24
    • 1242352070 scopus 로고    scopus 로고
    • Origin and phylogeny of chloroplasts revealed by a simple correlation analysis of complete genomes
    • Chu KH, Qi J, Yu ZG, Anh V, ((2004)) Origin and phylogeny of chloroplasts revealed by a simple correlation analysis of complete genomes. Mol Biol Evol 21:: 200--206.
    • (2004) Mol Biol Evol , vol.21 , pp. 200-206
    • Chu, K.H.1    Qi, J.2    Yu, Z.G.3    Anh, V.4
  • 25
    • 34047110724 scopus 로고    scopus 로고
    • Whole genome molecular phylogeny of large dsDNA viruses using composition vector method
    • Gao L, Qi J, ((2007)) Whole genome molecular phylogeny of large dsDNA viruses using composition vector method. BMC Evol Biol 7:: 41.
    • (2007) BMC Evol Biol , vol.7 , pp. 41
    • Gao, L.1    Qi, J.2
  • 26
    • 77953661117 scopus 로고    scopus 로고
    • Whole-proteome phylogeny of large dsDNA viruses and parvoviruses through a composition vector method related to dynamical language model
    • Yu ZG, Chu KH, Li CP, Anh V, Zhou LQ, et al. ((2010)) Whole-proteome phylogeny of large dsDNA viruses and parvoviruses through a composition vector method related to dynamical language model. BMC Evol Biol 10:: 192.
    • (2010) BMC Evol Biol , vol.10 , pp. 192
    • Yu, Z.G.1    Chu, K.H.2    Li, C.P.3    Anh, V.4    Zhou, L.Q.5
  • 27
    • 69949152972 scopus 로고    scopus 로고
    • A fungal phylogeny based on 82 complete genomes using the composition vector method
    • Wang H, Xu Z, Gao L, Hao B, ((2009)) A fungal phylogeny based on 82 complete genomes using the composition vector method. BMC Evol Biol 9:: 195.
    • (2009) BMC Evol Biol , vol.9 , pp. 195
    • Wang, H.1    Xu, Z.2    Gao, L.3    Hao, B.4
  • 28
    • 0023375195 scopus 로고
    • The neighbour-joining method: a new method for reconstructing phylogenetic trees
    • Saitou N, Nei M, ((1987)) The neighbour-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 10:: 471--483.
    • (1987) Mol Biol Evol , vol.10 , pp. 471-483
    • Saitou, N.1    Nei, M.2
  • 29
    • 0000122573 scopus 로고
    • PHYLIP-phylogeny inference package (version 3.2)
    • Felsenstein J, ((1989)) PHYLIP-phylogeny inference package (version 3.2). Cladistics 5:: 164--166.
    • (1989) Cladistics , vol.5 , pp. 164-166
    • Felsenstein, J.1
  • 30
    • 13244255415 scopus 로고    scopus 로고
    • MUSCLE: a multiple sequence alignment method with reduced time and space complexity
    • Edgar RC, ((2004)) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5:: 113.
    • (2004) BMC Bioinformatics , vol.5 , pp. 113
    • Edgar, R.C.1
  • 31
    • 79957613599 scopus 로고    scopus 로고
    • MEGA5: Molecular Evolutionary Genetics Analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods
    • Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. ((2011)) MEGA5: Molecular Evolutionary Genetics Analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:: 2731--2739.
    • (2011) Mol Biol Evol , vol.28 , pp. 2731-2739
    • Tamura, K.1    Peterson, D.2    Peterson, N.3    Stecher, G.4    Nei, M.5
  • 32
    • 0019296687 scopus 로고
    • A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
    • Kimura M, ((1980)) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:: 111--120.
    • (1980) J Mol Evol , vol.16 , pp. 111-120
    • Kimura, M.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.