메뉴 건너뛰기




Volumn 33, Issue 6, 2016, Pages 1635-1638

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data

Author keywords

Hypothesis testing; NCBI taxonomy; Phylogenetics; Phylogenomics; Tree comparison; tree visualization

Indexed keywords

DATA BASE; PHYLOGENOMICS; PHYLOGENY; TAXONOMY; BIOLOGICAL MODEL; BIOLOGY; GENETIC DATABASE; GENOMICS; INTERNET; MOLECULAR EVOLUTION; PROCEDURES; SEQUENCE ALIGNMENT; SOFTWARE;

EID: 84962897215     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msw046     Document Type: Article
Times cited : (1387)

References (30)
  • 1
    • 84937442075 scopus 로고    scopus 로고
    • Compact graphical representation of phylogenetic data and metadata with GraPhlAn
    • Asnicar F, Weingart G, Tickle TL, Huttenhower C, Segata N. 2015. Compact graphical representation of phylogenetic data and metadata with GraPhlAn. Peer J. 3:e1029
    • (2015) Peer J , vol.3 , pp. e1029
    • Asnicar, F.1    Weingart, G.2    Tickle, T.L.3    Huttenhower, C.4    Segata, N.5
  • 3
    • 3042842589 scopus 로고    scopus 로고
    • A maximum likelihood method for detecting functional divergence at individual codon sites, with application to gene family evolution
    • Bielawski JP, Yang Z. 2004. A maximum likelihood method for detecting functional divergence at individual codon sites, with application to gene family evolution. J. Mol. Evol. 59:121-132
    • (2004) J. Mol. Evol , vol.59 , pp. 121-132
    • Bielawski, J.P.1    Yang, Z.2
  • 5
    • 84858411861 scopus 로고    scopus 로고
    • Rooting the eukaryotic tree with mitochondrial and bacterial proteins
    • Derelle R, Lang BF. 2012. Rooting the eukaryotic tree with mitochondrial and bacterial proteins. Mol. Biol. Evol. 29:1277-1289
    • (2012) Mol. Biol. Evol , vol.29 , pp. 1277-1289
    • Derelle, R.1    Lang, B.F.2
  • 6
    • 0000122573 scopus 로고    scopus 로고
    • PHYLIP (phylogeny inference package)
    • Felsenstein J. 2005. PHYLIP (Phylogeny Inference Package). Cladistics 5:164-166
    • (2005) Cladistics , vol.5 , pp. 164-166
    • Felsenstein, J.1
  • 10
    • 84868007353 scopus 로고    scopus 로고
    • Dendroscope 3: An interactive tool for rooted phylogenetic trees and networks
    • Huson DH, Scornavacca C. 2012. Dendroscope 3: an interactive tool for rooted phylogenetic trees and networks. Syst. Biol. 61:1061-1067
    • (2012) Syst. Biol , vol.61 , pp. 1061-1067
    • Huson, D.H.1    Scornavacca, C.2
  • 13
    • 33845873289 scopus 로고    scopus 로고
    • Interactive Tree of Life (iTOL): An online tool for phylogenetic tree display and annotation
    • Letunic I, Bork P. 2007. Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics 23:127-128
    • (2007) Bioinformatics , vol.23 , pp. 127-128
    • Letunic, I.1    Bork, P.2
  • 14
    • 79961206352 scopus 로고    scopus 로고
    • TreeKO: A duplication-aware algorithm for the comparison of phylogenetic trees
    • Marcet-Houben M, Gabaldón T. 2011. TreeKO: A duplication-aware algorithm for the comparison of phylogenetic trees. Nucleic Acids Res. 39:e66
    • (2011) Nucleic Acids Res , vol.39 , pp. e66
    • Marcet-Houben, M.1    Gabaldón, T.2
  • 15
    • 84940653986 scopus 로고    scopus 로고
    • Beyond the whole-genome duplication: Phylogenetic evidence for an ancient interspecies hybridization in the baker's yeast lineage
    • Marcet-Houben M, Gabaldón T. 2015. Beyond the whole-genome duplication: phylogenetic evidence for an ancient interspecies hybridization in the baker's yeast lineage. PLoS Biol. 13(8):e1002220
    • (2015) PLoS Biol , vol.13 , Issue.8 , pp. e1002220
    • Marcet-Houben, M.1    Gabaldón, T.2
  • 16
    • 17444412589 scopus 로고    scopus 로고
    • Detecting amino acid sites under positive selection and purifying selection
    • Massingham T, Goldman N. 2005. Detecting amino acid sites under positive selection and purifying selection. Genetics 169:1753-1762
    • (2005) Genetics , vol.169 , pp. 1753-1762
    • Massingham, T.1    Goldman, N.2
  • 17
    • 1042304216 scopus 로고    scopus 로고
    • APE: Analyses of phylogenetics and evolution in R language
    • Paradis E, Claude J, Strimmer K. 2004. APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20:289-290
    • (2004) Bioinformatics , vol.20 , pp. 289-290
    • Paradis, E.1    Claude, J.2    Strimmer, K.3
  • 19
    • 0019424782 scopus 로고
    • Comparison of phylogenetic trees
    • Robinson DF, Foulds LR. 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
  • 20
    • 36448956752 scopus 로고    scopus 로고
    • The K tree score: Quantification of differences in the relative branch length and topology of phylogenetic trees
    • Soria-Carrasco V, Talavera G, Igea J, Castresana J. 2007. The K tree score: quantification of differences in the relative branch length and topology of phylogenetic trees. Bioinformatics 23:2954-2956
    • (2007) Bioinformatics , vol.23 , pp. 2954-2956
    • Soria-Carrasco, V.1    Talavera, G.2    Igea, J.3    Castresana, J.4
  • 21
    • 77954202497 scopus 로고    scopus 로고
    • DendroPy: A Python library for phylogenetic computing
    • Sukumaran J, Holder MT. 2010. DendroPy: a Python library for phylogenetic computing. Bioinformatics 26:1569-1571
    • (2010) Bioinformatics , vol.26 , pp. 1569-1571
    • Sukumaran, J.1    Holder, M.T.2
  • 23
    • 84865083935 scopus 로고    scopus 로고
    • Bio.Phylo: A unified toolkit for processing, analyzing and visualizing phylogenetic trees in Biopython
    • Talevich E, Invergo B, Cock P, Chapman B. 2012. Bio.Phylo: a unified toolkit for processing, analyzing and visualizing phylogenetic trees in Biopython. BMC Bioinformatics 13:209
    • (2012) BMC Bioinformatics , vol.13 , pp. 209
    • Talevich, E.1    Invergo, B.2    Cock, P.3    Chapman, B.4
  • 26
    • 34547803197 scopus 로고    scopus 로고
    • PAML 4: Phylogenetic analysis by maximum likelihood
    • Yang Z. 2007. PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24:1586-1591
    • (2007) Mol. Biol. Evol , vol.24 , pp. 1586-1591
    • Yang, Z.1
  • 27
    • 0036270185 scopus 로고    scopus 로고
    • Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages
    • Yang Z, Nielsen R. 2002. Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol. Biol. Evol. 19:908-917
    • (2002) Mol. Biol. Evol , vol.19 , pp. 908-917
    • Yang, Z.1    Nielsen, R.2
  • 28
    • 0034097381 scopus 로고    scopus 로고
    • Codon-substitution models for heterogeneous selection pressure at amino acid sites
    • Yang Z, Nielsen R, Goldman N, Pedersen AM. 2000. Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155:431-449
    • (2000) Genetics , vol.155 , pp. 431-449
    • Yang, Z.1    Nielsen, R.2    Goldman, N.3    Pedersen, A.M.4
  • 29
    • 84890044025 scopus 로고    scopus 로고
    • A general species delimitation method with applications to phylogenetic placements
    • Zhang J, Kapli P, Pavlidis P, Stamatakis A. 2013. A general species delimitation method with applications to phylogenetic placements. Bioinformatics 29:2869-2876
    • (2013) Bioinformatics , vol.29 , pp. 2869-2876
    • Zhang, J.1    Kapli, P.2    Pavlidis, P.3    Stamatakis, A.4
  • 30
    • 27844439855 scopus 로고    scopus 로고
    • Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level
    • Zhang J, Nielsen R, Yang Z. 2005. Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Mol. Biol. Evol. 22:2472-2479
    • (2005) Mol. Biol. Evol , vol.22 , pp. 2472-2479
    • Zhang, J.1    Nielsen, R.2    Yang, Z.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.