메뉴 건너뛰기




Volumn 29, Issue 6, 2012, Pages 1587-1598

Phylo-MCOA: A fast and efficient method to detect outlier genes and species in phylogenomics using multiple co-inertia analysis

Author keywords

Fungal genomes; Multivariate analysis; Outlier genes; Phylogenetic markers; Phylogenomics

Indexed keywords

ARTICLE; FUNGAL GENETICS; GENE IDENTIFICATION; GENETIC ANALYSIS; MULTIPLE CO INERTIA ANALYSIS; MULTIVARIATE ANALYSIS; NONHUMAN; PHYLOGENETIC TREE; PHYLOGENOMICS; SPECIES DIFFERENTIATION; SPECIES IDENTIFICATION;

EID: 84861368644     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msr317     Document Type: Article
Times cited : (63)

References (39)
  • 3
    • 0742284128 scopus 로고    scopus 로고
    • Multiple co-inertia analysis: A tool for assessing synchrony in the temporal variability of aquatic communities
    • DOI 10.1016/j.crvi.2003.10.007, PII S1631069103003354
    • Bady P, Doledec S, Dumont B, Fruget JF. 2004. Multiple co-inertia analysis: a tool for assessing synchrony in the temporal variability of aquatic communities. C R Biol. 327:29-36. (Pubitemid 38155309)
    • (2004) Comptes Rendus - Biologies , vol.327 , Issue.1 , pp. 29-36
    • Bady, P.1    Doledec, S.2    Dumont, B.3    Fruget, J.-F.4
  • 4
    • 41149095119 scopus 로고    scopus 로고
    • Using molecular markers and multivariate methods to study the genetic diversity of local European and Asian chicken breeds
    • DOI 10.1111/j.1365-2052.2008.01703.x
    • Berthouly C, Bed'Hom B, Tixier-Boichard M, Chen CF, Lee YP, Laloe D, Legros H, Verrier E, Rognon X. 2008. Using molecular markers and multivariate methods to study the genetic diversity of local European and Asian chicken breeds. Anim Genet. 39: 121-129. (Pubitemid 351441688)
    • (2008) Animal Genetics , vol.39 , Issue.2 , pp. 121-129
    • Berthouly, C.1    Bed'Hom, B.2    Tixier-Boichard, M.3    Chen, C.F.4    Lee, Y.P.5    Laloe, D.6    Legros, H.7    Verrier, E.8    Rognon, X.9
  • 5
    • 0036137155 scopus 로고    scopus 로고
    • Eubacterial phylogeny based on translational apparatus proteins
    • DOI 10.1016/S0168-9525(01)02522-7, PII S0168952501025227
    • Brochier C, Bapteste E, Moreira D, Philippe H. 2002. Eubacterial phylogeny based on translational apparatus proteins. Trends Genet. 18:1-5. (Pubitemid 34031845)
    • (2002) Trends in Genetics , vol.18 , Issue.1 , pp. 1-5
    • Brochier, C.1    Bapteste, E.2    Moreira, D.3    Philippe, H.4
  • 7
    • 0002037744 scopus 로고    scopus 로고
    • Analyses de la co-inertie de K nuages de points
    • Chessel D, Hanafi M. 1996. Analyses de la co-inertie de K nuages de points. Rev Stat Appl. 44:35-60.
    • (1996) Rev Stat Appl. , vol.44 , pp. 35-60
    • Chessel, D.1    Hanafi, M.2
  • 8
    • 34547482037 scopus 로고    scopus 로고
    • Summarizing a posterior distribution of trees using agreement subtrees
    • DOI 10.1080/10635150701485091, PII 780835555
    • Cranston KA, Rannala B. 2007. Summarizing a posterior distribution of trees using agreement subtrees. Syst Biol. 56:578-590. (Pubitemid 47171632)
    • (2007) Systematic Biology , vol.56 , Issue.4 , pp. 578-590
    • Cranston, K.A.1    Rannala, B.2
  • 9
    • 80054943881 scopus 로고    scopus 로고
    • The Euclidean nature of phylogenetic distance matrices
    • de Vienne DM, Aguileta G, Ollier S. 2011. The Euclidean nature of phylogenetic distance matrices. Syst Biol. 60:826-832.
    • (2011) Syst Biol. , vol.60 , pp. 826-832
    • De Vienne, D.M.1    Aguileta, G.2    Ollier, S.3
  • 10
    • 33646928341 scopus 로고    scopus 로고
    • Discordance of species trees with their most likely gene trees
    • DOI 10.1371/journal.pgen.0020068
    • Degnan JH, Rosenberg NA. 2006. Discordance of species trees with their most likely gene trees. PLoS Genet. 2:762-768. (Pubitemid 43794324)
    • (2006) PLoS Genetics , vol.2 , Issue.5 , pp. 762-768
    • Degnan, J.H.1    Rosenberg, N.A.2
  • 11
    • 37649004826 scopus 로고    scopus 로고
    • The ade4 package-II: Two-table and K-table methods
    • Dray S, Dufour AB, Chessel D. 2007. The ade4 package-II: two-table and K-table methods. R News. 7:47-52.
    • (2007) R News. , vol.7 , pp. 47-52
    • Dray, S.1    Dufour, A.B.2    Chessel, D.3
  • 13
    • 0000461280 scopus 로고
    • Confidence-limits on phylogenies-an approach using the bootstrap
    • Felsenstein J. 1985. Confidence-limits on phylogenies-an approach using the bootstrap. Evolution 39:783-791.
    • (1985) Evolution , vol.39 , pp. 783-791
    • Felsenstein, J.1
  • 15
    • 0000803938 scopus 로고
    • Consensus supertrees-the synthesis of rooted trees containing overlapping sets of labeled leaves
    • Gordon AD. 1986. Consensus supertrees-the synthesis of rooted trees containing overlapping sets of labeled leaves. J Classif. 3: 335-348.
    • (1986) J Classif. , vol.3 , pp. 335-348
    • Gordon, A.D.1
  • 16
    • 2642563943 scopus 로고
    • Distance matrices and their Euclidean approximation
    • Jambu M, Diday E, Lebart L, Pages J, Tomassone R, editors Amsterdam (The Netherlands): Elsevier
    • Gower JC. 1984. Distance matrices and their Euclidean approximation. In: Jambu M, Diday E, Lebart L, Pages J, Tomassone R, editors. Data analysis and informatics III. Amsterdam (The Netherlands): Elsevier. p. 3-21.
    • (1984) Data Analysis and Informatics III , pp. 3-21
    • Gower, J.C.1
  • 17
    • 33747044600 scopus 로고
    • Metric and Euclidean properties of dissimilarity coefficients
    • Gower JC, Legendre P. 1986. Metric and Euclidean properties of dissimilarity coefficients. J Classif. 3:5-48.
    • (1986) J Classif. , vol.3 , pp. 5-48
    • Gower, J.C.1    Legendre, P.2
  • 18
    • 33746747008 scopus 로고    scopus 로고
    • Specific functional signature in soil macro-invertebrate biostructures
    • DOI 10.1111/j.1365-2435.2005.01026.x
    • Hedde M, Lavelle P, Joffre R, Jimenez JJ, Decaens T. 2005. Specific functional signature in soil macro-invertebrate biostructures. Funct Ecol. 19:785-793. (Pubitemid 44933502)
    • (2005) Functional Ecology , vol.19 , Issue.5 , pp. 785-793
    • Hedde, M.1    Lavelle, P.2    Joffre, R.3    Jimenez, J.J.4    Decaens, T.5
  • 19
    • 22844442543 scopus 로고    scopus 로고
    • Analysis and visualization of tree space
    • DOI 10.1080/10635150590946961
    • Hillis DM, Heath TA, St John K. 2005. Analysis and visualization of tree space. Syst Biol. 54:471-482. (Pubitemid 41040445)
    • (2005) Systematic Biology , vol.54 , Issue.3 , pp. 471-482
    • Hillis, D.M.1    Heath, T.A.2    St. John, K.3
  • 20
    • 30744470609 scopus 로고    scopus 로고
    • Application of phylogenetic networks in evolutionary studies
    • DOI 10.1093/molbev/msj030
    • Huson DH, Bryant D. 2006. Application of phylogenetic networks in evolutionary studies. Mol Biol Evol. 23:254-267. (Pubitemid 43100040)
    • (2006) Molecular Biology and Evolution , vol.23 , Issue.2 , pp. 254-267
    • Huson, D.H.1    Bryant, D.2
  • 21
    • 35848948407 scopus 로고    scopus 로고
    • Consensus genetic structuring and typological value of markers using multiple co-inertia analysis
    • DOI 10.1051/gse:2007021
    • Laloe D, Jombart T, Dufour AB, Moazami-Goudarzi K. 2007. Consensus genetic structuring and typological value of markers using multiple co-inertia analysis. Genet Sel Evol. 39:545-567. (Pubitemid 350057067)
    • (2007) Genetics Selection Evolution , vol.39 , Issue.5 , pp. 545-567
    • Laloe, D.1    Jombart, T.2    Dufour, A.-B.3    Moazami-Goudarzi, K.4
  • 22
    • 80051792622 scopus 로고    scopus 로고
    • Let them fall where they may: Congruence analysis in massive, phylogenetically messy datasets
    • Leigh JW, Schliep K, Lopez P, Bapteste E. 2011. Let them fall where they may: congruence analysis in massive, phylogenetically messy datasets. Mol Biol Evol. 28:2773-2785.
    • (2011) Mol Biol Evol. , vol.28 , pp. 2773-2785
    • Leigh, J.W.1    Schliep, K.2    Lopez, P.3    Bapteste, E.4
  • 25
    • 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(10):e66.
    • (2011) Nucleic Acids Res. , vol.39 , Issue.10
    • Marcet-Houben, M.1    Gabaldón, T.2
  • 26
    • 57649207907 scopus 로고    scopus 로고
    • FUNYBASE: A FUNgal phYlogenomic dataBASE
    • (11 co-authors)
    • Marthey S, Aguileta G, Rodolphe F, et al. (11 co-authors). 2008. FUNYBASE: a FUNgal phYlogenomic dataBASE. BMC Bioinformatics. 9:456.
    • (2008) BMC Bioinformatics. , vol.9 , pp. 456
    • Marthey, S.1    Aguileta, G.2    Rodolphe, F.3
  • 27
    • 1042304216 scopus 로고    scopus 로고
    • APE: Analyses of phylogenetics and evolution in R language
    • DOI 10.1093/bioinformatics/btg412
    • Paradis E, Claude J, Strimmer K. 2004. APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20:289-290. (Pubitemid 38195693)
    • (2004) Bioinformatics , vol.20 , Issue.2 , pp. 289-290
    • Paradis, E.1    Claude, J.2    Strimmer, K.3
  • 30
    • 0036515730 scopus 로고    scopus 로고
    • The probability of topological concordance of gene trees and species trees
    • DOI 10.1006/tpbi.2001.1568
    • Rosenberg NA. 2002. The probability of topological concordance of gene trees and species trees. Theor Popul Biol. 61:225-247. (Pubitemid 38042804)
    • (2002) Theoretical Population Biology , vol.61 , Issue.2 , pp. 225-247
    • Rosenberg, N.A.1
  • 31
    • 34248188251 scopus 로고    scopus 로고
    • SCaFoS: A tool for selection, concatenation and fusion of sequences for phylogenomics
    • Roure B, Rodriguez-Ezpeleta N, Philippe H. 2007. SCaFoS: a tool for selection, concatenation and fusion of sequences for phylogenomics. BMC Evol Biol. 7(1 Suppl):S2.
    • (2007) BMC Evol Biol. , vol.7 , Issue.1 SUPPL.
    • Roure, B.1    Rodriguez-Ezpeleta, N.2    Philippe, H.3
  • 32
    • 0032030505 scopus 로고    scopus 로고
    • Phylogenetic supertrees: Assembling the trees of life
    • DOI 10.1016/S0169-5347(97)01242-1
    • Sanderson MJ, Purvis A, Henze C. 1998. Phylogenetic supertrees: assembling the trees of life. Trends Ecol Evol. 13:105-109. (Pubitemid 28136253)
    • (1998) Trends in Ecology and Evolution , vol.13 , Issue.3 , pp. 105-109
    • Sanderson, M.J.1    Purvis, A.2    Henze, C.3
  • 35
    • 33750403801 scopus 로고    scopus 로고
    • RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
    • DOI 10.1093/bioinformatics/btl446
    • Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688-2690. (Pubitemid 44642609)
    • (2006) Bioinformatics , vol.22 , Issue.21 , pp. 2688-2690
    • Stamatakis, A.1
  • 36
    • 20444410815 scopus 로고    scopus 로고
    • Stochastic models for horizontal gene transfer: Taking a random walk through tree space
    • DOI 10.1534/genetics.103.025692
    • Suchard MA. 2005. Stochastic models for horizontal gene transfer: taking a random walk through tree space. Genetics 170:419-431. (Pubitemid 40800003)
    • (2005) Genetics , vol.170 , Issue.1 , pp. 419-431
    • Suchard, M.A.1
  • 38
    • 33646584164 scopus 로고    scopus 로고
    • Visualizing and assessing phylogenetic congruence of core gene sets: A case study of the γ-proteobacteria
    • DOI 10.1093/molbev/msj113
    • Susko E, Leigh J, Doolittle WF, Bapteste E. 2006. Visualizing and assessing phylogenetic congruence of core gene sets: a case study of the gamma-proteobacteria. Mol Biol Evol. 23:1019-1030. (Pubitemid 43726067)
    • (2006) Molecular Biology and Evolution , vol.23 , Issue.5 , pp. 1019-1030
    • Susko, E.1    Leigh, J.2    Doolittle, W.F.3    Bapteste, E.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.