-
1
-
-
57649209055
-
Assessing the performance of single-copy genes for recovering robust phylogenies
-
Aguileta G, Marthey S, Chiapello H, Lebrun MH, Rodolphe F, Fournier E, Gendrault-Jacquemard A, Giraud T. 2008. Assessing the performance of single-copy genes for recovering robust phylogenies. Syst Biol. 57:613-627.
-
(2008)
Syst Biol.
, vol.57
, pp. 613-627
-
-
Aguileta, G.1
Marthey, S.2
Chiapello, H.3
Lebrun, M.H.4
Rodolphe, F.5
Fournier, E.6
Gendrault-Jacquemard, A.7
Giraud, T.8
-
2
-
-
33846839390
-
Bayesian estimation of concordance among gene trees
-
DOI 10.1093/molbev/msl170
-
Ane C, Larget B, Baum DA, Smith SD, Rokas A. 2007. Bayesian estimation of concordance among gene trees. Mol Biol Evol. 24: 412-426. (Pubitemid 46204374)
-
(2007)
Molecular Biology and Evolution
, vol.24
, Issue.2
, pp. 412-426
-
-
Ane, C.1
Larget, B.2
Baum, D.A.3
Smith, S.D.4
Rokas, A.5
-
3
-
-
0742284128
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
28
-
-
79953716259
-
Resolving difficult phylogenetic questions: Why more sequences are not enough
-
Philippe H, Brinkmann H, Lavrov DV, Littlewood DTJ, Manuel M, Wörheide G, Baurain D. 2011. Resolving difficult phylogenetic questions: why more sequences are not enough. PLoS Biol. 9: e1000602.
-
(2011)
PLoS Biol.
, vol.9
-
-
Philippe, H.1
Brinkmann, H.2
Lavrov, D.V.3
Littlewood, D.T.J.4
Manuel, M.5
Wörheide, G.6
Baurain, D.7
-
29
-
-
33847656285
-
Detecting and overcoming systematic Errors in genome-scale phylogenies
-
DOI 10.1080/10635150701397643, PII 778977148
-
Rodriguez-Ezpeleta N, Brinkmann H, Roure B, Lartillot N, Lang BF, Philippe H. 2007. Detecting and overcoming systematic errors in genome-scale phylogenies. Syst Biol. 56:389-399. (Pubitemid 46826902)
-
(2007)
Systematic Biology
, vol.56
, Issue.3
, pp. 389-399
-
-
Rodreguez-Ezpeleta, N.1
Brinkmann, H.2
Roure, B.3
Lartillot, N.4
Lang, B.F.5
Philippe, H.6
-
30
-
-
0036515730
-
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
-
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
-
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
-
34
-
-
58849142045
-
Concatenated analysis sheds light on early metazoan evolution and fuels a modern "urmetazoon" hypothesis
-
Schierwater B, Eitel M, Jakob W, Osigus H-J, Hadrys H, Dellaporta SL, Kolokotronis S-O, DeSalle R. 2009. Concatenated analysis sheds light on early metazoan evolution and fuels a modern "urmetazoon" hypothesis. PLoS Biol. 7:e1000020.
-
(2009)
PLoS Biol.
, vol.7
-
-
Schierwater, B.1
Eitel, M.2
Jakob, W.3
Osigus, H.-J.4
Hadrys, H.5
Dellaporta, S.L.6
Kolokotronis, S.-O.7
Desalle, R.8
-
35
-
-
33750403801
-
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
-
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
-
37
-
-
0242679448
-
Evolutionary similarity among genes
-
DOI 10.1198/016214503000000558
-
Suchard MA, Weiss RE, Sinsheimer JS, Dorman KS, Patel M, McCabe ERB. 2003. Evolutionary similarity among genes. J Am Stat Assoc. 98:653-662. (Pubitemid 37395936)
-
(2003)
Journal of the American Statistical Association
, vol.98
, Issue.463
, pp. 653-662
-
-
Suchard, M.A.1
Weiss, R.E.2
Sinsheimer, J.S.3
Dorman, K.S.4
Patel, M.5
McCabe, E.R.B.6
-
38
-
-
33646584164
-
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
-
39
-
-
35748976874
-
Treeness triangles: Visualizing the loss of phylogenetic signal
-
White WT, Hills SF, Gaddam R, Holland BR, Penny D. 2007. Treeness triangles: visualizing the loss of phylogenetic signal. Mol Biol Evol. 24:2029-2039.
-
(2007)
Mol Biol Evol.
, vol.24
, pp. 2029-2039
-
-
White, W.T.1
Hills, S.F.2
Gaddam, R.3
Holland, B.R.4
Penny, D.5
|