-
1
-
-
9744231340
-
Dissection of phylogenetic relationships among 19 rapidly growing Mycobacterium species by 16S rRNA, hsp65, sodA, recA and rpoB gene sequencing
-
Adékambi, T. & Drancourt, M. (2004). Dissection of phylogenetic relationships among 19 rapidly growing Mycobacterium species by 16S rRNA, hsp65, sodA, recA and rpoB gene sequencing. Int J Syst Evol Microbiol 54, 2095-2105.
-
(2004)
Int J Syst Evol Microbiol
, vol.54
, pp. 2095-2105
-
-
Adékambi, T.1
Drancourt, M.2
-
2
-
-
0037329391
-
Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence
-
Alfaro, M. E., Zoller, S. & Lutzoni, F. (2003). Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence. Mol Biol Evol 20, 255-266.
-
(2003)
Mol Biol Evol
, vol.20
, pp. 255-266
-
-
Alfaro, M.E.1
Zoller, S.2
Lutzoni, F.3
-
3
-
-
0036206183
-
Leuconostoc ficulneum sp. nov., a novel lactic acid bacterium isolated from a ripe fig, and reclassification of Lactobacillus fructosus as Leuconostoc fructosum comb. nov
-
Antunes, A., Rainey, F. A., Nobre, M. F., Schumann, P., Ferreira, A. M., Ramos, A., Santos, H. & da Costa, M. S. (2002). Leuconostoc ficulneum sp. nov., a novel lactic acid bacterium isolated from a ripe fig, and reclassification of Lactobacillus fructosus as Leuconostoc fructosum comb. nov. Int J Syst Evol Microbiol 52, 647-655.
-
(2002)
Int J Syst Evol Microbiol
, vol.52
, pp. 647-655
-
-
Antunes, A.1
Rainey, F.A.2
Nobre, M.F.3
Schumann, P.4
Ferreira, A.M.5
Ramos, A.6
Santos, H.7
da Costa, M.S.8
-
4
-
-
9944255059
-
Partitioned Bayesian analyses, partition choice, and the phylogenetic relationships of scincid lizards
-
Brandley, M. C., Schmitz, A. & Reeder, T. W. (2005). Partitioned Bayesian analyses, partition choice, and the phylogenetic relationships of scincid lizards. Syst Biol 54, 373-390.
-
(2005)
Syst Biol
, vol.54
, pp. 373-390
-
-
Brandley, M.C.1
Schmitz, A.2
Reeder, T.W.3
-
5
-
-
12044257391
-
Partitioning and combining data in phylogenetic analysis
-
Bull, J. J., Huelsenbeck, J. P., Cunningham, C. W., Swofford, D. L. & Waddell, P. J. (1993). Partitioning and combining data in phylogenetic analysis. Syst Biol 42, 384-397.
-
(1993)
Syst Biol
, vol.42
, pp. 384-397
-
-
Bull, J.J.1
Huelsenbeck, J.P.2
Cunningham, C.W.3
Swofford, D.L.4
Waddell, P.J.5
-
6
-
-
3242695950
-
Data partitions and complex models in Bayesian analysis: The phylogeny of gymnophtalmid lizards
-
Castoe, T. A., Doan, T. M. & Parkinson, C. L. (2004). Data partitions and complex models in Bayesian analysis: the phylogeny of gymnophtalmid lizards. Syst Biol 53, 448-469.
-
(2004)
Syst Biol
, vol.53
, pp. 448-469
-
-
Castoe, T.A.1
Doan, T.M.2
Parkinson, C.L.3
-
7
-
-
0026010926
-
Phylogenetic analysis of the genus Lactobacillus and related lactic acid bacteria as determined by reverse transcriptase sequencing of 16S rRNA
-
Collins, M. D., Rodrigues, U., Aguirre, M., Farrow, J., Martinez-Murcia, A., Phillips, B., Williams, A. & Wallbanks, S. (1991). Phylogenetic analysis of the genus Lactobacillus and related lactic acid bacteria as determined by reverse transcriptase sequencing of 16S rRNA. FEMS Microbiol Lett 77, 5-12.
-
(1991)
FEMS Microbiol Lett
, vol.77
, pp. 5-12
-
-
Collins, M.D.1
Rodrigues, U.2
Aguirre, M.3
Farrow, J.4
Martinez-Murcia, A.5
Phillips, B.6
Williams, A.7
Wallbanks, S.8
-
8
-
-
0027768689
-
Taxonomic studies on some leuconostoc-like organisms from fermented sausages: Description of a new genus Weissella for the Leuconostoc paramesenteroides group of species
-
Collins, M. D., Samells, J., Metaxopoulos, J. & Wallbanks, S. (1993). Taxonomic studies on some leuconostoc-like organisms from fermented sausages: description of a new genus Weissella for the Leuconostoc paramesenteroides group of species. J Appl Bacteriol 75, 595-603.
-
(1993)
J Appl Bacteriol
, vol.75
, pp. 595-603
-
-
Collins, M.D.1
Samells, J.2
Metaxopoulos, J.3
Wallbanks, S.4
-
9
-
-
0028936112
-
Proposal to reclassify Leuconostoc oenos as Oenococcus oeni gen. nov., comb. nov
-
Dicks, L. M. T., Dellaglio, F. E. & Collins, M. D. (1995). Proposal to reclassify Leuconostoc oenos as Oenococcus oeni gen. nov., comb. nov. Int J Syst Bacteriol 45, 395-397.
-
(1995)
Int J Syst Bacteriol
, vol.45
, pp. 395-397
-
-
Dicks, L.M.T.1
Dellaglio, F.E.2
Collins, M.D.3
-
10
-
-
84959798530
-
Cases in which parsimony or compatibility methods will be positively misleading
-
Felsenstein, J. (1978). Cases in which parsimony or compatibility methods will be positively misleading. Syst Zool 27, 401-410.
-
(1978)
Syst Zool
, vol.27
, pp. 401-410
-
-
Felsenstein, J.1
-
11
-
-
0003437299
-
PHYLIP (phylogenetic inference package), version 3.6a
-
Distributed by the author. Department of Genome Sciences, University of Washington, Seattle, USA
-
Felsenstein, J. (2002). PHYLIP (phylogenetic inference package), version 3.6a. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle, USA.
-
(2002)
-
-
Felsenstein, J.1
-
12
-
-
0017143034
-
Hybridization between the deoxyribonucleic acids of some strains of heterofermentative lactic acid bacteria
-
Garvie, E. I. (1976). Hybridization between the deoxyribonucleic acids of some strains of heterofermentative lactic acid bacteria. Int J Syst Bacteriol 26, 116-122.
-
(1976)
Int J Syst Bacteriol
, vol.26
, pp. 116-122
-
-
Garvie, E.I.1
-
13
-
-
0019770522
-
Sub-divisions within the genus Leuconostoc as shown by RNA/DNA hybridization
-
Garvie, E. I. (1981). Sub-divisions within the genus Leuconostoc as shown by RNA/DNA hybridization. J Gen Microbiol 127, 209-212.
-
(1981)
J Gen Microbiol
, vol.127
, pp. 209-212
-
-
Garvie, E.I.1
-
14
-
-
0034351387
-
Likelihood-based tests of topologies in phylogenetics
-
Goldman, N., Anderson, J. P. & Rodrigo, A. G. (2000). Likelihood-based tests of topologies in phylogenetics. Syst Biol 49, 652-670.
-
(2000)
Syst Biol
, vol.49
, pp. 652-670
-
-
Goldman, N.1
Anderson, J.P.2
Rodrigo, A.G.3
-
16
-
-
0029113744
-
The robustness of two phylogenetic methods: Four-taxon simulations reveal a slight superiority of maximum likelihood over neighbor joining
-
Huelsenbeck, J. P. (1995). The robustness of two phylogenetic methods: four-taxon simulations reveal a slight superiority of maximum likelihood over neighbor joining. Mol Biol Evol 12, 843-849.
-
(1995)
Mol Biol Evol
, vol.12
, pp. 843-849
-
-
Huelsenbeck, J.P.1
-
17
-
-
12044255023
-
Success of phylogenetic methods in the four-taxon case
-
Huelsenbeck, J. P. & Hillis, D. M. (1993). Success of phylogenetic methods in the four-taxon case. Syst Biol 42, 247-264.
-
(1993)
Syst Biol
, vol.42
, pp. 247-264
-
-
Huelsenbeck, J.P.1
Hillis, D.M.2
-
18
-
-
0034849408
-
MrBayes: Bayesian inference of phylogenetic trees
-
Huelsenbeck, J. P. & Ronquist F. R. (2001). MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics 17, 754-755.
-
(2001)
Bioinformatics
, vol.17
, pp. 754-755
-
-
Huelsenbeck, J.P.1
Ronquist, F.R.2
-
19
-
-
0000219186
-
Regular, nonsporing gram-positive rods
-
In Edited by P. H. A. Sneath, N. S. Mair, M. E. Sharpe & J. G. Holt. Baltimore: Williams & Wilkins
-
Kandler, O. & Weiss, N. (1986). Regular, nonsporing gram-positive rods. In Bergey's Manual of Systematic Bacteriology, vol. 2, pp. 1208-1234. Edited by P. H. A. Sneath, N. S. Mair, M. E. Sharpe & J. G. Holt. Baltimore: Williams & Wilkins.
-
(1986)
Bergey's Manual of Systematic Bacteriology
, vol.2
, pp. 1208-1234
-
-
Kandler, O.1
Weiss, N.2
-
20
-
-
24944587193
-
Towards a genome-based taxonomy for prokaryotes
-
Konstantinidis, K. T. & Tiedje, J. M. (2005). Towards a genome-based taxonomy for prokaryotes. J Bacteriol 187, 6258-6264.
-
(2005)
J Bacteriol
, vol.187
, pp. 6258-6264
-
-
Konstantinidis, K.T.1
Tiedje, J.M.2
-
21
-
-
0021277009
-
A new method for calculating evolutionary substitution rates
-
Lanave, C., Preparata, G., Saccone, C. & Serio, G. (1984). A new method for calculating evolutionary substitution rates. J Mol Evol 20, 86-93.
-
(1984)
J Mol Evol
, vol.20
, pp. 86-93
-
-
Lanave, C.1
Preparata, G.2
Saccone, C.3
Serio, G.4
-
22
-
-
0025982062
-
Construction of T-vectors, a rapid and general system for direct cloning of unmodified PCR products
-
Marchuk, D., Drumm, M., Saulino, A. & Collins, F. (1991). Construction of T-vectors, a rapid and general system for direct cloning of unmodified PCR products. Nucleic Acids Res 19, 1154.
-
(1991)
Nucleic Acids Res
, vol.19
, pp. 1154
-
-
Marchuk, D.1
Drumm, M.2
Saulino, A.3
Collins, F.4
-
23
-
-
0025707918
-
A phylogenetic analysis of the genus Leuconostoc based on reverse transcriptase sequencing of 16S rRNA
-
Martinez-Murcia, A. J. & Collins, M. D. (1990). A phylogenetic analysis of the genus Leuconostoc based on reverse transcriptase sequencing of 16S rRNA. FEMS Microbiol Lett 70, 73-84.
-
(1990)
FEMS Microbiol Lett
, vol.70
, pp. 73-84
-
-
Martinez-Murcia, A.J.1
Collins, M.D.2
-
24
-
-
0027300577
-
Phylogenetic analysis of some leuconostocs and related organisms as determined from large-subunit rRNA gene sequences: Assessment of congruence of small- and large-subunit rRNA derived trees
-
Martinez-Murcia, A. J., Harland, N. M. & Collins, M. D. (1993). Phylogenetic analysis of some leuconostocs and related organisms as determined from large-subunit rRNA gene sequences: assessment of congruence of small- and large-subunit rRNA derived trees. J Appl Bacteriol 74, 532-541.
-
(1993)
J Appl Bacteriol
, vol.74
, pp. 532-541
-
-
Martinez-Murcia, A.J.1
Harland, N.M.2
Collins, M.D.3
-
25
-
-
23944514505
-
Genomic analysis of Oenococcus oeni PSU-1 and its relevance to winemaking
-
Mills, D. A., Rawsthorne, H., Parker, C., Tamir, D. & Makarova, K. (2005). Genomic analysis of Oenococcus oeni PSU-1 and its relevance to winemaking. FEMS Microbiol Rev 29, 465-475.
-
(2005)
FEMS Microbiol Rev
, vol.29
, pp. 465-475
-
-
Mills, D.A.1
Rawsthorne, H.2
Parker, C.3
Tamir, D.4
Makarova, K.5
-
26
-
-
0029798105
-
Analysis of the beta subunit of DNA-dependent RNA polymerase does not support the hypothesis inferred from 16S rRNA analysis that Oenococcus oeni (formerly Leuconostoc oenos) is a tachytelic (fast-evolving) bacterium
-
Morse, R., Collins, M. D., O'Hanlon, K., Wallbanks, S. & Richardson, P. T. (1996). Analysis of the beta subunit of DNA-dependent RNA polymerase does not support the hypothesis inferred from 16S rRNA analysis that Oenococcus oeni (formerly Leuconostoc oenos) is a tachytelic (fast-evolving) bacterium. Int J Syst Bacteriol 46, 1004-1009.
-
(1996)
Int J Syst Bacteriol
, vol.46
, pp. 1004-1009
-
-
Morse, R.1
Collins, M.D.2
O'Hanlon, K.3
Wallbanks, S.4
Richardson, P.T.5
-
27
-
-
0036739151
-
Phylogenetic, amino acid content and indel analyses of the β subunit of DNA-dependent RNA polymerase of Gram-positive and Gram-negative bacteria
-
Morse, R., O'Hanlon, K. & Collins, M. D. (2002). Phylogenetic, amino acid content and indel analyses of the β subunit of DNA-dependent RNA polymerase of Gram-positive and Gram-negative bacteria. Int J Syst Evol Microbiol 52, 1477-1484.
-
(2002)
Int J Syst Evol Microbiol
, vol.52
, pp. 1477-1484
-
-
Morse, R.1
O'Hanlon, K.2
Collins, M.D.3
-
28
-
-
27744488568
-
Heterotachy and long-branch attraction in phylogenetics
-
Philippe, H., Zhou, Y., Brinkmann, H., Rodrigue, N. & Delsuc, F. (2005). Heterotachy and long-branch attraction in phylogenetics. BMC Evol Biol 5, 50.
-
(2005)
BMC Evol Biol
, vol.5
, pp. 50
-
-
Philippe, H.1
Zhou, Y.2
Brinkmann, H.3
Rodrigue, N.4
Delsuc, F.5
-
29
-
-
0024553747
-
Rapid extraction of bacterial genomic DNA with guanidium thiocyanate
-
Pitcher, D. G., Sanders, N. A. & Owen, R. J. (1989). Rapid extraction of bacterial genomic DNA with guanidium thiocyanate. Lett Appl Microbiol 8, 151-156.
-
(1989)
Lett Appl Microbiol
, vol.8
, pp. 151-156
-
-
Pitcher, D.G.1
Sanders, N.A.2
Owen, R.J.3
-
30
-
-
0031773680
-
Modeltest: Testing the model of DNA substitution
-
Posada, D. & Crandall, K. A. (1998). Modeltest: testing the model of DNA substitution. Bioinfiormatics 14, 817-818.
-
(1998)
Bioinfiormatics
, vol.14
, pp. 817-818
-
-
Posada, D.1
Crandall, K.A.2
-
31
-
-
0032766857
-
Multiple comparisons of log-likelihoods with applications to phylogenetic: Inference
-
Shimodaira, H. & Hasegawa, M. (1999). Multiple comparisons of log-likelihoods with applications to phylogenetic: inference. Mol Biol Evol 16, 1114-1116.
-
(1999)
Mol Biol Evol
, vol.16
, pp. 1114-1116
-
-
Shimodaira, H.1
Hasegawa, M.2
-
32
-
-
0035989633
-
Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology
-
& other authors
-
Stackebrandt, E., Frederiksen, W., Garrity, G. M., Grimont P. A. D., Kämpfer, P., Maiden, M. C. J., Nesme, X., Rosselló-Mora, R., Swings, J. & other authors (2002). Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 52, 1043-1047.
-
(2002)
Int J Syst Evol Microbiol
, vol.52
, pp. 1043-1047
-
-
Stackebrandt, E.1
Frederiksen, W.2
Garrity, G.M.3
Grimont, P.A.D.4
Kämpfer, P.5
Maiden, M.C.J.6
Nesme, X.7
Rosselló-Mora, R.8
Swings, J.9
-
34
-
-
0027157960
-
Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees
-
Tamura, K. & Nei, M. (1993). Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10, 512-526.
-
(1993)
Mol Biol Evol
, vol.10
, pp. 512-526
-
-
Tamura, K.1
Nei, M.2
-
35
-
-
0027968068
-
CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
-
Thompson, J. D., Higgins, D. G. & Gibson, T. J. (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22, 4673-4680.
-
(1994)
Nucleic Acids Res
, vol.22
, pp. 4673-4680
-
-
Thompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
-
36
-
-
0028948030
-
PCR amplification and direct sequencing of gyrB genes with universal primers and their application to the detection and taxonomic analysis of Pseudomonas putida strains
-
Yamamoto, S. & Harayama, S. (1995). PCR amplification and direct sequencing of gyrB genes with universal primers and their application to the detection and taxonomic analysis of Pseudomonas putida strains. Appl Environ Microbiol 61, 1104-1109.
-
(1995)
Appl Environ Microbiol
, vol.61
, pp. 1104-1109
-
-
Yamamoto, S.1
Harayama, S.2
-
37
-
-
0031827993
-
Phylogenetic relationships of Pseudomonas putida strains deduced from the nucleotide sequences of gyrB, rpoD and 16S rRNA genes
-
Yamamoto, S. & Harayama, S. (1998). Phylogenetic relationships of Pseudomonas putida strains deduced from the nucleotide sequences of gyrB, rpoD and 16S rRNA genes. Int J Syst Bacteriol 48, 813-819.
-
(1998)
Int J Syst Bacteriol
, vol.48
, pp. 813-819
-
-
Yamamoto, S.1
Harayama, S.2
-
38
-
-
0029970097
-
Maximum-likelihood models for combined analyses of multiple sequence data
-
Yang, Z. (1996). Maximum-likelihood models for combined analyses of multiple sequence data. J Mol Evol 42, 587-596.
-
(1996)
J Mol Evol
, vol.42
, pp. 587-596
-
-
Yang, Z.1
-
39
-
-
0024322776
-
Phylogenetic structure of the "leuconostocs": An interesting case of a rapidly evolving organism
-
Yang, D. & Woese, C. R. (1989). Phylogenetic structure of the "leuconostocs": an interesting case of a rapidly evolving organism. Syst Appl Microbiol 12, 145-149.
-
(1989)
Syst Appl Microbiol
, vol.12
, pp. 145-149
-
-
Yang, D.1
Woese, C.R.2
|