-
1
-
-
34248350454
-
Phylogeographic support for horizontal gene transfer involving sympatric bruchid species
-
Alvarez, N., B. Benrey, M. Hossaert-McKey, A. Grill, D. McKey, and N. Galtier. 2006. Phylogeographic support for horizontal gene transfer involving sympatric bruchid species. Biol. Direct. 1:21.
-
(2006)
Biol. Direct.
, vol.1
, pp. 21
-
-
Alvarez, N.1
Benrey, B.2
Hossaert-Mckey, M.3
Grill, A.4
McKey, D.5
Galtier, N.6
-
2
-
-
4444353678
-
Phylogenetic reconstruction and lateral gene transfer
-
DOI 10.1016/j.tim.2004.07.002, PII S0966842X04001593
-
Bapteste, E., Y. Boucher, J. Leigh, and W. F. Doolittle. 2004. Phylogenetic reconstruction and lateral gene transfer. Trends Microbiol. 12:406- 411. (Pubitemid 39178591)
-
(2004)
Trends in Microbiology
, vol.12
, Issue.9
, pp. 406-411
-
-
Bapteste, E.1
Boucher, Y.2
Leigh, J.3
Doolittle, W.F.4
-
3
-
-
21644441587
-
Do orthologous gene phylogenies really support tree-thinking?
-
Bapteste, E, E. Susko, J. Leigh, D. MacLeod, R. L. Charlebois, and W. F. Doolittle. 2005. Do orthologous gene phylogenies really support tree-thinking? BMC Evol. Biol. 5:33.
-
(2005)
BMC Evol. Biol.
, vol.5
, pp. 33
-
-
Bapteste, E.1
Susko, E.2
Leigh, J.3
MacLeod, D.4
Charlebois, R.L.5
Doolittle, W.F.6
-
5
-
-
0037819441
-
Widespread horizontal transfer of mitochondrial genes in flowering plants
-
DOI 10.1038/nature01743
-
Bergthorsson, U., K. L. Adams, B. Thomason, and J. D. Palmer. 2003. Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424:197-201. (Pubitemid 36858687)
-
(2003)
Nature
, vol.424
, Issue.6945
, pp. 197-201
-
-
Bergthorsson, U.1
Adams, K.L.2
Thomason, B.3
Palmer, J.D.4
-
6
-
-
0036137155
-
Eubacterial phylogeny based on translational apparatus proteins
-
DOI 10.1016/S0168-9525(01)02522-7, PII S0168952501025227
-
Brochier, C, E. Bapteste, D. Moreira, and H. Philippe. 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
-
-
0034942865
-
Universal trees based on large combined protein sequence data sets
-
DOI 10.1038/90129
-
Brown, J. R., C. J. Douady, M. J. Italia, W. E. Marshall, and M. J. Stanhope. 2001. Universal trees based on large combined protein sequence data sets. Nat. Genet. 28:281-285. (Pubitemid 32626033)
-
(2001)
Nature Genetics
, vol.28
, Issue.3
, pp. 281-285
-
-
Brown, J.R.1
Douady, C.J.2
Italia, M.J.3
Marshall, W.E.4
Stanhope, M.J.5
-
8
-
-
0030802669
-
The sequences of heat shock protein 40 (DNAJ) homologs provide evidence for a close evolutionary relationship between the deinococcus-thermus group and cyanobacteria
-
DOI 10.1007/PL00006219
-
Bustard, K., and R. S. Gupta. 1997. The sequences of heat shock protein 40 (DnaJ) homologs provide evidence for a close evolutionary relationship between the Deinococcus-Thermus group and cyanobacteria. J. Mol. Evol. 45:193-205. (Pubitemid 27323525)
-
(1997)
Journal of Molecular Evolution
, vol.45
, Issue.2
, pp. 193-205
-
-
Bustard, K.1
Gupta, R.S.2
-
9
-
-
21244469784
-
Horizontal transfer of two operons coding for hydrogenases between bacteria and archaea
-
DOI 10.1007/s00239-004-0094-8
-
Calteau, A., M. Gouy, and G. Perriere. 2005. Horizontal transfer of two operons coding for hydrogenases between bacteria and archaea. J. Mol. Evol. 60:557-565. (Pubitemid 40896555)
-
(2005)
Journal of Molecular Evolution
, vol.60
, Issue.5
, pp. 557-565
-
-
Calteau, A.1
Gouy, M.2
Perriere, G.3
-
10
-
-
0036061865
-
A phylogenomic approach to bacterial phylogeny: Evidence of a core of genes sharing a common history
-
DOI 10.1101/gr.187002
-
Daubin, V., M. Gouy, and G. Perriere. 2002. A phylogenomic approach to bacterial phylogeny: Evidence of a core of genes sharing a common history. Genome Res. 12:1080-1090. (Pubitemid 34785201)
-
(2002)
Genome Research
, vol.12
, Issue.7
, pp. 1080-1090
-
-
Daubin, V.1
Gouy, M.2
Perriere, G.3
-
11
-
-
0042027842
-
Phylogenetics and the cohesion of bacterial genomes
-
DOI 10.1126/science.1086568
-
Daubin, V., N. A. Moran, and H. Ochman. 2003. Phylogenetics and the cohesion of bacterial genomes. Science 301:829-832. (Pubitemid 36962623)
-
(2003)
Science
, vol.301
, Issue.5634
, pp. 829-832
-
-
Daubin, V.1
Moran, N.A.2
Ochman, H.3
-
12
-
-
1242284664
-
Quartet mapping and the extent of lateral transfer in bacterial genomes
-
DOI 10.1093/molbev/msg234
-
Daubin, V., and H. Ochman. 2004. Quartet mapping and the extent of lateral transfer in bacterial genomes. Mol. Biol. Evol. 21:86- 89. (Pubitemid 38233521)
-
(2004)
Molecular Biology and Evolution
, vol.21
, Issue.1
, pp. 86-89
-
-
Daubin, V.1
Ochman, H.2
-
13
-
-
0033603539
-
Phylogenetic classification and the universal tree
-
Doolittle, W. F. 1999. Phylogenetic classification and the universal tree. Science 284:2124-2129.
-
(1999)
Science
, vol.284
, pp. 2124-2129
-
-
Doolittle, W.F.1
-
14
-
-
33745955637
-
Bio++, a set of c++ libraries for sequence analysis, phylogenetics, population genetics and molecular evolution
-
Dutheil, J., S. Gaillard, E. Bazin, S. Glemin, V. Ranwez, N. Galtier, and K. Belkhir. 2006. Bio++, a set of C++ libraries for sequence analysis, phylogenetics, population genetics and molecular evolution. BMC Bioinformatics 7:188.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 188
-
-
Dutheil, J.1
Gaillard, S.2
Bazin, E.3
Glemin, S.4
Ranwez, V.5
Galtier, N.6
Belkhir, K.7
-
15
-
-
0035029534
-
Maximum-likelihood phylogenetic analysis under a covarion-like model
-
Galtier, N. 2001. Maximum-likelihood phylogenetic analysis under a covarion-like model. Mol. Biol. Evol.18:866-873. (Pubitemid 32372956)
-
(2001)
Molecular Biology and Evolution
, vol.18
, Issue.5
, pp. 866-873
-
-
Galtier, N.1
-
16
-
-
0028106613
-
Molecular phylogeny of Eubacteria: A new multiple tree analysis method applied to 15 sequence data sets questions the monophyly of Gram-positive bacteria
-
DOI 10.1016/0923-2508(94)90030-2
-
Galtier, N., and M. Gouy. 1994. Molecular phylogeny of Eubacteria: A new multiple tree analysis method applied to 15 sequence data sets questions the monophyly of gram-positive bacteria. Res. Microbiol. 145:531-541. (Pubitemid 24296197)
-
(1994)
Research in Microbiology
, vol.145
, Issue.7
, pp. 531-541
-
-
Galtier, N.1
Gouy, M.2
-
17
-
-
26444580130
-
The cobweb of life revealed by genome-scale estimates of horizontal gene transfer
-
Ge, F., L. S. Wang, and J. Kim. 2005. The cobweb of life revealed by genome-scale estimates of horizontal gene transfer. PloS Biol. 3:e316.
-
(2005)
PloS Biol.
, vol.3
-
-
Ge, F.1
Wang, L.S.2
Kim, J.3
-
19
-
-
0242578620
-
A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
-
DOI 10.1080/10635150390235520
-
Guindon, S., and O. Gascuel. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704. (Pubitemid 37365050)
-
(2003)
Systematic Biology
, vol.52
, Issue.5
, pp. 696-704
-
-
Guindon, S.1
Gascuel, O.2
-
20
-
-
0034077901
-
A compound Poisson process for relaxing the molecular clock
-
Huelsenbeck, J. P., B. Larget, and D. Swofford. 2000. A compound Poisson process for relaxing the molecular clock. Genetics 154:1879-1892. (Pubitemid 30211265)
-
(2000)
Genetics
, vol.154
, Issue.4
, pp. 1879-1892
-
-
Huelsenbeck, J.P.1
Larget, B.2
Swofford, D.3
-
21
-
-
0037248815
-
OGRe: A relational database for comparative analysis of mitochondrial genomes
-
DOI 10.1093/nar/gkg077
-
Jameson, D., A. P. Gibson, C. Hudelot, and P. G. Higgs. 2003. OGRe: A relational database for comparative analysis of mitochondrial genomes. Nucleic Acids Res. 31:202-206. (Pubitemid 36150365)
-
(2003)
Nucleic Acids Research
, vol.31
, Issue.1
, pp. 202-206
-
-
Jameson, D.1
Gibson, A.P.2
Hudelot, C.3
Higgs, P.G.4
-
22
-
-
33750418625
-
Maximum likelihood of phylogenetic networks
-
DOI 10.1093/bioinformatics/btl452
-
Jin, G., L. Nakhleh, S. Snir, and T. Tuller. 2006. Maximum likelihood of phylogenetic networks. Bioinformatics 22:2604-2611. (Pubitemid 44642598)
-
(2006)
Bioinformatics
, vol.22
, Issue.21
, pp. 2604-2611
-
-
Jin, G.1
Nakhleh, L.2
Snir, S.3
Tuller, T.4
-
23
-
-
0026691182
-
The rapid generation of mutation data matrices from protein sequences
-
Jones, D. T, W. R. Taylor, and J. M. Thornton. 1992. The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 8:275-282.
-
(1992)
Comput. Appl. Biosci.
, vol.8
, pp. 275-282
-
-
Jones, D.T.1
Taylor, W.R.2
Thornton, J.M.3
-
25
-
-
1342271382
-
From gene trees to organismal phylogeny in prokaryotes: The case of the gamma- Proteobacteria
-
Lerat, E., V. Daubin, and N. A. Moran. 2003. From gene trees to organismal phylogeny in prokaryotes: The case of the gamma- Proteobacteria. PLoS Biol. I:el9.
-
(2003)
PLoS Biol.
, vol.1
-
-
Lerat, E.1
Daubin, V.2
Moran, N.A.3
-
26
-
-
21844434913
-
Evolutionary origins of genomic repertoires in bacteria
-
Lerat, E, V. Daubin, H. Ochman, and N. A. Moran. 2005. Evolutionary origins of genomic repertoires in bacteria. PLoS Biol. 3:el30.
-
(2005)
PLoS Biol.
, vol.3
-
-
Lerat, E.1
Daubin, V.2
Ochman, H.3
Moran, N.A.4
-
27
-
-
0027359258
-
Evolution of the recA gene and the molecular phylogeny of bacteria
-
Lloyd, A. T., and P. M. Sharp. 1993. Evolution of the recA gene and the molecular phylogeny of bacteria. J. Mol. Evol. 37:399-407. (Pubitemid 23283725)
-
(1993)
Journal of Molecular Evolution
, vol.37
, Issue.4
, pp. 399-407
-
-
Lloyd, A.T.1
Sharp, P.M.2
-
28
-
-
18944369385
-
Deduction of probable events of lateral gene transfer through comparison of phylogenetic trees by recursive consolidation and rearrangement
-
MacLeod, D., R. L. Charlebois, F. Doolittle, and E. Bapteste. 2005. Deduction of probable events of lateral gene transfer through comparison of phylogenetic trees by recursive consolidation and rearrangement. BMC Evol. Biol. 5:27.
-
(2005)
BMC Evol. Biol.
, vol.5
, pp. 27
-
-
MacLeod, D.1
Charlebois, R.L.2
Doolittle, F.3
Bapteste, E.4
-
29
-
-
0031504952
-
Gene trees in species trees
-
Maddison, W. P. 1997. Gene trees in species trees. Syst. Biol. 46:523-536.
-
(1997)
Syst. Biol.
, vol.46
, pp. 523-536
-
-
Maddison, W.P.1
-
30
-
-
17744386162
-
Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and protostomia
-
DOI 10.1093/molbev/msi111
-
Philippe, H., N. Lartillot, and H. Brinkmann. 2005. Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia. Mol. Biol. Evol. 22:1246-1253. (Pubitemid 40577762)
-
(2005)
Molecular Biology and Evolution
, vol.22
, Issue.5
, pp. 1246-1253
-
-
Philippe, H.1
Lartillot, N.2
Brinkmann, H.3
-
31
-
-
0026822436
-
Phylogenetic inference based on matrix representation of trees
-
Ragan, M. A. 1992. Phylogenetic inference based on matrix representation of trees. Mol. Phylogenet. Evol. 1:53-58.
-
(1992)
Mol. Phylogenet. Evol.
, vol.1
, pp. 53-58
-
-
Ragan, M.A.1
-
32
-
-
0035142366
-
Mitochondrial versus nuclear gene sequences in deep-level mammalian phylogeny reconstruction
-
Springer, M. S., R. W. DeBry, C. Douady, H. M. Amrine, O. Madsen, W. W. de Jong, and M. J. Stanhope. 2001. Mitochondrial versus nuclear gene sequences in deep-level mammalian phylogeny reconstruction. Mol. Biol. Evol. 18:132-143. (Pubitemid 32118858)
-
(2001)
Molecular Biology and Evolution
, vol.18
, Issue.2
, pp. 132-143
-
-
Springer, M.S.1
DeBry, R.W.2
Douady, C.3
Amrine, H.M.4
Madsen, O.5
De Jong, W.W.6
Stanhope, M.J.7
-
33
-
-
3343020196
-
Molecules consolidate the placental mammal tree
-
DOI 10.1016/j.tree.2004.05.006, PII S0169534704001429
-
Springer, M. S., M. J. Stanhope, O. Madsen, W. W. de Jong. 2004. Molecules consolidate the placental mammal tree. Trends Ecol. Evol. 19:430-438. (Pubitemid 38991669)
-
(2004)
Trends in Ecology and Evolution
, vol.19
, Issue.8
, pp. 430-438
-
-
Springer, M.S.1
Stanhope, M.J.2
Madsen, O.3
De Jong, W.W.4
-
34
-
-
20444410815
-
Stochastic models for horizontal gene transfer: Taking a random walk through tree space
-
DOI 10.1534/genetics.103.025692
-
Suchard, M. A. 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
-
35
-
-
33646584164
-
Visualizing and assessing phylogenetic congruence of core gene sets: A case study of the γ-proteobacteria
-
DOI 10.1093/molbev/msj113
-
Susko, E., J. Leigh, W. F. Doolittle, and E. Bapteste. 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
-
36
-
-
0023184331
-
Bacterial evolution
-
Woese, C. R. 1987. Bacterial evolution. Microbiol. Rev. 51:221-271. (Pubitemid 17082512)
-
(1987)
Microbiological Reviews
, vol.51
, Issue.2
, pp. 221-271
-
-
Woese, C.R.1
-
38
-
-
0348044549
-
Genome trees constructed using five different approaches suggest new major bacterial clades
-
Wolf, Y. I., I. B. Rogozin, N. V. Grishin, R. L. Tatusov, and E. V. Koonin. 2001. Genome trees constructed using five different approaches suggest new major bacterial clades. BMC Evol. Biol. 1:8.
-
(2001)
BMC Evol. Biol.
, vol.1
, pp. 8
-
-
Wolf, Y.I.1
Rogozin, I.B.2
Grishin, N.V.3
Tatusov, R.L.4
Koonin, E.V.5
-
39
-
-
1942422301
-
Genome mosaicism and organismal lineages
-
DOI 10.1016/j.tig.2004.03.009, PII S0168952504000770
-
Zhaxybayeva, O., P. Lapierre, and J. P. Gogarten. 2004. Genome mosaicism and organismal lineages. Trends Genet. 20:254-260. (Pubitemid 38510439)
-
(2004)
Trends in Genetics
, vol.20
, Issue.5
, pp. 254-260
-
-
Zhaxybayeva, O.1
Lapierre, P.2
Gogarten, J.P.3
|