메뉴 건너뛰기




Volumn 7, Issue 2, 2012, Pages

A format for phylogenetic placements

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER PROGRAM; DATA ANALYSIS; GENE MAPPING; INFORMATION PROCESSING; MAXIMUM LIKELIHOOD METHOD; PARSIMONY ANALYSIS; PHYLOGENETIC PLACEMENT; PHYLOGENETIC TREE; PHYLOGENY; SEQUENCE ANALYSIS; ALGORITHM; BIOLOGY; COMPUTER INTERFACE; COMPUTER LANGUAGE; DNA SEQUENCE; HUMAN; METHODOLOGY; REPRODUCIBILITY; SEQUENCE ALIGNMENT; STATISTICAL MODEL;

EID: 84857490160     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0031009     Document Type: Article
Times cited : (52)

References (16)
  • 1
    • 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
  • 2
    • 84963036271 scopus 로고
    • Quantitative phyletics and the evolution of anurans
    • Kluge A, Farris J, (1969) Quantitative phyletics and the evolution of anurans. Syst Zool 18: 1-32.
    • (1969) Syst Zool , vol.18 , pp. 1-32
    • Kluge, A.1    Farris, J.2
  • 3
    • 48249105419 scopus 로고    scopus 로고
    • Taxonomic distribution of large DNA viruses in the sea
    • Monier A, Claverie J, Ogata H, (2008) Taxonomic distribution of large DNA viruses in the sea. Genome Biol 9: R106.
    • (2008) Genome Biol , vol.9
    • Monier, A.1    Claverie, J.2    Ogata, H.3
  • 4
    • 33847291893 scopus 로고    scopus 로고
    • Quantitative phylogenetic assessment of microbial communities in diverse environments
    • Von Mering C, Hugenholtz P, Raes J, Tringe S, Doerks T, et al. (2007) Quantitative phylogenetic assessment of microbial communities in diverse environments. Science 315: 1126.
    • (2007) Science , vol.315 , pp. 1126
    • Von Mering, C.1    Hugenholtz, P.2    Raes, J.3    Tringe, S.4    Doerks, T.5
  • 5
    • 79955456912 scopus 로고    scopus 로고
    • Performance, accuracy, and web server for evolutionary placement of short sequence reads under maximum likelihood
    • Berger S, Krompass D, Stamatakis A, (2011) Performance, accuracy, and web server for evolutionary placement of short sequence reads under maximum likelihood. Syst Biol 60: 291.
    • (2011) Syst Biol , vol.60 , pp. 291
    • Berger, S.1    Krompass, D.2    Stamatakis, A.3
  • 6
    • 77958610660 scopus 로고    scopus 로고
    • pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree
    • Matsen F, Kodner R, Armbrust E, (2010) pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree. BMC Bioinfo 11: 538.
    • (2010) BMC Bioinfo , vol.11 , pp. 538
    • Matsen, F.1    Kodner, R.2    Armbrust, E.3
  • 7
    • 77955179934 scopus 로고    scopus 로고
    • MLTreeMap-accurate Maximum Likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogenies
    • Stark M, Berger S, Stamatakis A, von Mering C, (2010) MLTreeMap-accurate Maximum Likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogenies. BMC Genomics 11: 461.
    • (2010) BMC Genomics , vol.11 , pp. 461
    • Stark, M.1    Berger, S.2    Stamatakis, A.3    von Mering, C.4
  • 9
    • 55649110049 scopus 로고    scopus 로고
    • A simple, fast, and accurate method of phylogenomic inference
    • Wu M, Eisen J, (2008) A simple, fast, and accurate method of phylogenomic inference. Genome Biol 9: 1-11.
    • (2008) Genome Biol , vol.9 , pp. 1-11
    • Wu, M.1    Eisen, J.2
  • 10
    • 84857467559 scopus 로고    scopus 로고
    • The phylogenetic Kantorovich-Rubinstein metric for environmental sequence samples
    • Arxiv preprint. arXiv:1005.1699
    • Evans S, Matsen F, (2010) The phylogenetic Kantorovich-Rubinstein metric for environmental sequence samples. Arxiv preprint. arXiv:1005.1699.
    • (2010)
    • Evans, S.1    Matsen, F.2
  • 11
    • 84857467562 scopus 로고    scopus 로고
    • Edge principal components and squash clustering: using the special structure of phylogenetic placement data for sample comparison
    • arXiv: 1107.5095v1
    • Matsen F, Hoffman N, Evans S, (2011) Edge principal components and squash clustering: using the special structure of phylogenetic placement data for sample comparison. arXiv: 1107.5095v1.
    • (2011)
    • Matsen, F.1    Hoffman, N.2    Evans, S.3
  • 12
    • 80054886632 scopus 로고    scopus 로고
    • TopiaryExplorer: Visualizing large phylogenetic trees with environmental metadata
    • doi: 10.1093/bioinformatics/btr517
    • Pirrung M, Kennedy R, Caporaso J, Stombaugh J, Wendel D, et al. (2011) TopiaryExplorer: Visualizing large phylogenetic trees with environmental metadata. Bioinformatics doi:10.1093/bioinformatics/btr517.
    • (2011) Bioinformatics
    • Pirrung, M.1    Kennedy, R.2    Caporaso, J.3    Stombaugh, J.4    Wendel, D.5
  • 13
    • 79960414804 scopus 로고    scopus 로고
    • Aligning short reads to reference alignments and trees
    • Berger S, Stamatakis A, (2011) Aligning short reads to reference alignments and trees. Bioinformatics 27: 2068-2075.
    • (2011) Bioinformatics , vol.27 , pp. 2068-2075
    • Berger, S.1    Stamatakis, A.2
  • 14
    • 84864010118 scopus 로고    scopus 로고
    • SEPP: SATé-Enabled Phylogenetic Placement
    • Pacific Symposium on Biocomputing (PSB 2012). Jan 3-7, 2012, Hawaii
    • Mirarab S, Nguyen N, Warnow T, (2012) SEPP: SATé-Enabled Phylogenetic Placement. Pacific Symposium on Biocomputing (PSB 2012). Jan 3-7, 2012, Hawaii.
    • (2012)
    • Mirarab, S.1    Nguyen, N.2    Warnow, T.3
  • 15
    • 36949039971 scopus 로고    scopus 로고
    • The application/json Media Type for JavaScript Object Notation (JSON). RFC
    • Available:. Accessed 2012 Jan 27
    • Crockford D, (2006) The application/json Media Type for JavaScript Object Notation (JSON). RFC. Available: http://tools.ietf.org/html/rfc4627. Accessed 2012 Jan 27.
    • (2006)
    • Crockford, D.1
  • 16
    • 84857475221 scopus 로고    scopus 로고
    • An alignment-free generalization to indels of Felsenstein's phylogenetic pruning algorithm
    • Arxiv preprint. arXiv:11034347
    • Westesson O, Lunter G, Paten B, Holmes I, (2011) An alignment-free generalization to indels of Felsenstein's phylogenetic pruning algorithm. Arxiv preprint. arXiv:11034347.
    • (2011)
    • Westesson, O.1    Lunter, G.2    Paten, B.3    Holmes, I.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.