메뉴 건너뛰기




Volumn 3, Issue 1, 2008, Pages

Noisy: Identification of problematic columns in multiple sequence alignments

Author keywords

[No Author keywords available]

Indexed keywords


EID: 47949097485     PISSN: None     EISSN: 17487188     Source Type: Journal    
DOI: 10.1186/1748-7188-3-7     Document Type: Article
Times cited : (120)

References (37)
  • 1
    • 33744993430 scopus 로고    scopus 로고
    • Multiple Sequence Alignment Accuracy and Phylogenetic Inference
    • 10.1080/10635150500541730 16611602
    • Ogden TH Rosenberg M Multiple Sequence Alignment Accuracy and Phylogenetic Inference Syst Biol 2006, 55:314-328. 10.1080/ 10635150500541730 16611602
    • (2006) Syst Biol , vol.55 , pp. 314-328
    • Ogden, T.H.1    Rosenberg, M.2
  • 2
    • 34548088457 scopus 로고    scopus 로고
    • Heads or tails: A simple reliability check for multiple sequence alignments
    • 10.1093/molbev/msm060 17387100
    • Landan G Graur D Heads or tails: A simple reliability check for multiple sequence alignments Mol Biol Evol 2007, 24:1380-1383. 10.1093/molbev/ msm060 17387100
    • (2007) Mol Biol Evol , vol.24 , pp. 1380-1383
    • Landan, G.1    Graur, D.2
  • 3
    • 0000583137 scopus 로고    scopus 로고
    • Are Third Positions Really That Bad? A Test Using Vertebrate Cytochrome b
    • Björklund M Are Third Positions Really That Bad? A Test Using Vertebrate Cytochrome b Cladistics 1999, 15:91-97.
    • (1999) Cladistics , vol.15 , pp. 91-97
    • Björklund, M.1
  • 4
    • 0032028624 scopus 로고    scopus 로고
    • On the best evolutionary rate for phylogenetic analysis
    • 10.1080/106351598261067 12064232
    • Yang Z On the best evolutionary rate for phylogenetic analysis Syst Biol 1998, 47:125-133. 10.1080/106351598261067 12064232
    • (1998) Syst Biol , vol.47 , pp. 125-133
    • Yang, Z.1
  • 6
    • 84963056475 scopus 로고
    • A method of selection of characters in numerical taxonomy
    • 10.2307/2412604
    • Le Quesne WJ A method of selection of characters in numerical taxonomy Syst Zool 1969, 18:201-205. 10.2307/2412604
    • (1969) Syst Zool , vol.18 , pp. 201-205
    • Le Quesne, W.J.1
  • 7
    • 0003945705 scopus 로고
    • Consensus compatibility and missing data in phylogenetic inference
    • PhD thesis University of Bristol, UK
    • Wilkinson M Consensus compatibility and missing data in phylogenetic inference PhD thesis University of Bristol, UK 1992.
    • (1992)
    • Wilkinson, M.1
  • 8
    • 0028317340 scopus 로고
    • Phylogenetic relationships at the basal radiation of angiosperms: Further study by probability of character compatibility
    • 10.2307/2419774
    • Meachem CA Phylogenetic relationships at the basal radiation of angiosperms: Further study by probability of character compatibility Syst Bot 1994, 19:506-522. 10.2307/2419774
    • (1994) Syst Bot , vol.19 , pp. 506-522
    • Meachem, C.A.1
  • 9
    • 12444313041 scopus 로고    scopus 로고
    • Identifying and removing fast-evolving sites using compatibility analysis: An example from the arthropoda
    • 10.1080/10635150490888877 15764565
    • Pisani D Identifying and removing fast-evolving sites using compatibility analysis: An example from the arthropoda Syst Biol 2004, 53:978-989. 10.1080/10635150490888877 15764565
    • (2004) Syst Biol , vol.53 , pp. 978-989
    • Pisani, D.1
  • 10
    • 0028064845 scopus 로고
    • Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods
    • 10.1007/BF00160154 7932792
    • Yang Z Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods J Mol Evol 1994, 39:306-314. 10.1007/BF00160154 7932792
    • (1994) J Mol Evol , vol.39 , pp. 306-314
    • Yang, Z.1
  • 11
    • 0033859839 scopus 로고    scopus 로고
    • Phylogeny of 33 ribosomal and six other proteins encoded in an ancient gene cluster that is conserved across prokaryotic genomes: Influence of excluding poorly alignable sites from analysis
    • 10939673
    • Hansmann S Martin W Phylogeny of 33 ribosomal and six other proteins encoded in an ancient gene cluster that is conserved across prokaryotic genomes: Influence of excluding poorly alignable sites from analysis Int J Syst Evol Microbiol 2000, 50:1655-1663. 10939673
    • (2000) Int J Syst Evol Microbiol , vol.50 , pp. 1655-1663
    • Hansmann, S.1    Martin, W.2
  • 12
    • 0033015732 scopus 로고    scopus 로고
    • Archaea sister group of Bacteria? Indications from tree reconstruction artifacts in ancient phylogenies
    • 10368959
    • Brinkmann H Philippe H Archaea sister group of Bacteria? Indications from tree reconstruction artifacts in ancient phylogenies Mol Biol Evol 1999, 16:817-825. 10368959
    • (1999) Mol Biol Evol , vol.16 , pp. 817-825
    • Brinkmann, H.1    Philippe, H.2
  • 13
    • 34047267637 scopus 로고
    • A Canonical Decomposition Theory for Metrics on a Finite Set
    • 10.1016/0001-8708(92)90061-O
    • Bandelt HJ Dress AWM A Canonical Decomposition Theory for Metrics on a Finite Set Adv Math 1992, 92:47-105. 10.1016/0001-8708(92)90061-O
    • (1992) Adv Math , vol.92 , pp. 47-105
    • Bandelt, H.J.1    Dress, A.W.M.2
  • 14
    • 0031678692 scopus 로고    scopus 로고
    • SplitsTree: Analyzing and visualizing evolutionary data
    • 10.1093/bioinformatics/14.1.68 9520503
    • Huson DH SplitsTree: Analyzing and visualizing evolutionary data Bioinformatics 1998, 14:68-73. 10.1093/bioinformatics/14.1.68 9520503
    • (1998) Bioinformatics , vol.14 , pp. 68-73
    • Huson, D.H.1
  • 15
    • 2442636143 scopus 로고    scopus 로고
    • Cyclic permutations and evolutionary trees
    • 10.1016/S0196-8858(03)00098-8
    • Semple C Steel M Cyclic permutations and evolutionary trees Adv Appl Math 2004, 32:669-680. 10.1016/S0196-8858(03)00098-8
    • (2004) Adv Appl Math , vol.32 , pp. 669-680
    • Semple, C.1    Steel, M.2
  • 16
    • 0002074731 scopus 로고
    • The Recovery of Trees from Measures of Dissimilarity
    • Edinburgh, UK: Edinburgh University Press Hodson FR, Kendall DG, Tautu P
    • Buneman P The Recovery of Trees from Measures of Dissimilarity Mathematics and the Archeological and Historical Sciences Edinburgh, UK: Edinburgh University Press Hodson FR, Kendall DG, Tautu P 1971:387-395.
    • (1971) Mathematics and the Archeological and Historical Sciences , pp. 387-395
    • Buneman, P.1
  • 17
    • 0026911267 scopus 로고
    • Split Decomposition: A New and Useful Approach to Phylogenetic Analysis of Distance Data
    • 10.1016/1055-7903(92)90021-8 1342941
    • Bandelt HJ Dress AWM Split Decomposition: A New and Useful Approach to Phylogenetic Analysis of Distance Data Mol Phylogenet Evol 1992, 1(3):242-252. 10.1016/1055-7903(92)90021-8 1342941
    • (1992) Mol Phylogenet Evol , vol.1 , Issue.3 , pp. 242-252
    • Bandelt, H.J.1    Dress, A.W.M.2
  • 18
    • 0002915858 scopus 로고
    • Zur Visualisierung abstrakter Ähnlichkeitsbeziehungen
    • PhD thesis Bielefeld University, Germany
    • Wetzel R Zur Visualisierung abstrakter Ähnlichkeitsbeziehungen PhD thesis Bielefeld University, Germany 1995.
    • (1995)
    • Wetzel, R.1
  • 19
    • 1542347067 scopus 로고    scopus 로고
    • Neighbor-Net: An Agglomerative Method for the Construction of Phylogenetic Networks
    • 10.1093/molbev/msh018 14660700
    • Bryant D Moulton V Neighbor-Net: An Agglomerative Method for the Construction of Phylogenetic Networks Mol Biol Evol 2004, 21:255-265. 10.1093/molbev/msh018 14660700
    • (2004) Mol Biol Evol , vol.21 , pp. 255-265
    • Bryant, D.1    Moulton, V.2
  • 20
    • 0034942558 scopus 로고    scopus 로고
    • Quartet-Mapping, a generalization of the likelihood mapping procedure
    • 11420361
    • Nieselt-Struwe K von Haeseler A Quartet-Mapping, a generalization of the likelihood mapping procedure Mol Biol Evol 2001, 18:1204-1219. 11420361
    • (2001) Mol Biol Evol , vol.18 , pp. 1204-1219
    • Nieselt-Struwe, K.1    von Haeseler, A.2
  • 21
    • 33846785301 scopus 로고    scopus 로고
    • QNet: An agglomerative method for the construction of phylogenetic networks from weighted quartets
    • 10.1093/molbev/msl180 17119010
    • Grünewald S Forslund K Dress AWM Moulton V QNet: An agglomerative method for the construction of phylogenetic networks from weighted quartets Mol Biol Evol 2007, 24:532-538. 10.1093/molbev/msl180 17119010
    • (2007) Mol Biol Evol , vol.24 , pp. 532-538
    • Grünewald, S.1    Forslund, K.2    Dress, A.W.M.3    Moulton, V.4
  • 22
    • 34547900812 scopus 로고    scopus 로고
    • Consistency of Neighbor-Net
    • 10.1186/1748-7188-2-8
    • Bryant D Moulton V Consistency of Neighbor-Net Alg Mol Biol 2007, 2:8. 10.1186/1748-7188-2-8
    • (2007) Alg Mol Biol , vol.2 , pp. 8
    • Bryant, D.1    Moulton, V.2
  • 23
    • 47949129128 scopus 로고    scopus 로고
    • Consistency of the QNet algorithm for generating planar split networks from weighted quartets
    • to appear
    • Grünewald S Moulton V Spillner A Consistency of the QNet algorithm for generating planar split networks from weighted quartets Disc Appl Math 2007. to appear
    • (2007) Disc Appl Math
    • Grünewald, S.1    Moulton, V.2    Spillner, A.3
  • 24
    • 0031599142 scopus 로고    scopus 로고
    • Mersenne Twister: A 623-dimensionally equidistributed uniform pseudorandom number generator
    • 10.1145/272991.272995
    • Matsumoto M Mersenne Twister: A 623-dimensionally equidistributed uniform pseudorandom number generator ACM Trans Modeling Comp Simulation 1998, 8:3-30. 10.1145/272991.272995
    • (1998) ACM Trans Modeling Comp Simulation , vol.8 , pp. 3-30
    • Matsumoto, M.1
  • 25
    • 28844503272 scopus 로고    scopus 로고
    • Phylogenetic relationships of spatangoid sea urchins (Echinoidea): Taxon sampling density and congruence between morphological and molecular estimates
    • 10.1111/j.1463-6409.2005.00201.x
    • Stockley B Smith AB Littlewood T Lessios HA Mackenzie-Dodds JA Phylogenetic relationships of spatangoid sea urchins (Echinoidea): Taxon sampling density and congruence between morphological and molecular estimates Zool Scripta 2005, 34:447-468. 10.1111/j.1463-6409.2005.00201.x
    • (2005) Zool Scripta , vol.34 , pp. 447-468
    • Stockley, B.1    Smith, A.B.2    Littlewood, T.3    Lessios, H.A.4    Mackenzie-Dodds, J.A.5
  • 27
    • 84963036271 scopus 로고
    • Quantitative phyletics and the evolution of anurans
    • 10.2307/2412407
    • Kluge AG Farris JS Quantitative phyletics and the evolution of anurans Syst Zool 1969, 18:1-32. 10.2307/2412407
    • (1969) Syst Zool , vol.18 , pp. 1-32
    • Kluge, A.G.1    Farris, J.S.2
  • 28
    • 84983540175 scopus 로고
    • The retention index and the rescaled consistency index
    • Farris JS The retention index and the rescaled consistency index Cladistics 1989, 5:417-419.
    • (1989) Cladistics , vol.5 , pp. 417-419
    • Farris, J.S.1
  • 30
    • 84860785038 scopus 로고    scopus 로고
    • Electronic Supplement http://www.bioinf.uni-leipzig.de/Publications/ SUPPLEMENTS/06-013/
    • Electronic Supplement
  • 31
    • 0028251187 scopus 로고
    • Evolution, Weighting, and Phylogenetic Utility of Mitochondrial Gene Sequences and a Compilation of Conserved Polymerase Chain Reaction Primers
    • Simon C Frati F Beckenbach A Crespi B Liu H Flook P Evolution, Weighting, and Phylogenetic Utility of Mitochondrial Gene Sequences and a Compilation of Conserved Polymerase Chain Reaction Primers Ann Entomol Soc Am 1994, 87:651-701.
    • (1994) Ann Entomol Soc Am , vol.87 , pp. 651-701
    • Simon, C.1    Frati, F.2    Beckenbach, A.3    Crespi, B.4    Liu, H.5    Flook, P.6
  • 32
    • 0027055554 scopus 로고
    • Signal, Noise, and Reliability in Molecular Phylogenetic Analysis
    • 1624764
    • Hillis DM Huelsenbeck JP Signal, Noise, and Reliability in Molecular Phylogenetic Analysis J Hered 1992, 83(3):189-195. 1624764
    • (1992) J Hered , vol.83 , Issue.3 , pp. 189-195
    • Hillis, D.M.1    Huelsenbeck, J.P.2
  • 33
    • 0023375195 scopus 로고
    • The neighbor-joining method: A new method for reconstructing phylogenetic trees
    • 3447015
    • Saitou N Nei M The neighbor-joining method: A new method for reconstructing phylogenetic trees Mol Biol Evol 1987, 4:406-425. 3447015
    • (1987) Mol Biol Evol , vol.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 34
    • 0000461280 scopus 로고
    • Confidence limits on phylogenies: An approach using the bootstrap
    • 10.2307/2408678
    • Felsenstein J Confidence limits on phylogenies: An approach using the bootstrap Evolution 1985, 31:783-791. 10.2307/2408678
    • (1985) Evolution , vol.31 , pp. 783-791
    • Felsenstein, J.1
  • 35
    • 0029982849 scopus 로고    scopus 로고
    • Bootstrap confidence levels for phylogenetic trees
    • 38940 8692949 10.1073/pnas.93.14.7085
    • Efron B Halloran E Holmes S Bootstrap confidence levels for phylogenetic trees Proc Natl Acad Sci USA 1996, 93:7085-7090. 38940 8692949 10.1073/ pnas.93.14.7085
    • (1996) Proc Natl Acad Sci USA , vol.93 , pp. 7085-7090
    • Efron, B.1    Halloran, E.2    Holmes, S.3
  • 36
    • 28944454501 scopus 로고    scopus 로고
    • DNA Assembly With Gaps (Dawg): Simulating Sequence Evolution
    • 10.1093/bioinformatics/bti1200 16306390
    • Cartwright R DNA Assembly With Gaps (Dawg): Simulating Sequence Evolution Bioinformatics 2005, 21(Suppl 3):iIi31-iii38. 10.1093/ bioinformatics/bti1200 16306390
    • (2005) Bioinformatics , vol.21 , Issue.SUPPL. 3
    • Cartwright, R.1
  • 37
    • 9644284416 scopus 로고    scopus 로고
    • Interrelationships of Staphyliniform groups inferred from 18S and 28S rDNA sequences, with special emphasis on Hydrophiloidea (Coleoptera, Staphyliniformia)
    • 10.1111/j.1439-0469.2004.00282.x
    • Korte A Ribera I Beutel RG Bernhard D Interrelationships of Staphyliniform groups inferred from 18S and 28S rDNA sequences, with special emphasis on Hydrophiloidea (Coleoptera, Staphyliniformia) J Zool Syst Evol Research 2004, 42:281-288. 10.1111/j.1439-0469.2004.00282.x
    • (2004) J Zool Syst Evol Research , vol.42 , pp. 281-288
    • Korte, A.1    Ribera, I.2    Beutel, R.G.3    Bernhard, D.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.