-
1
-
-
58549084151
-
A comparison of homologous recombination rates in bacteria and archaea
-
10.1038/ismej.2008.93, 18830278
-
Vos M, Didelot X. A comparison of homologous recombination rates in bacteria and archaea. ISME J 2009, 3:199-208. 10.1038/ismej.2008.93, 18830278.
-
(2009)
ISME J
, vol.3
, pp. 199-208
-
-
Vos, M.1
Didelot, X.2
-
2
-
-
53849111617
-
Evolution, population structure, and phylogeography of genetically monomorphic bacterial pathogens
-
10.1146/annurev.micro.62.081307.162832, 18785837
-
Achtman M. Evolution, population structure, and phylogeography of genetically monomorphic bacterial pathogens. Annu Rev Microbiol 2008, 62:53-70. 10.1146/annurev.micro.62.081307.162832, 18785837.
-
(2008)
Annu Rev Microbiol
, vol.62
, pp. 53-70
-
-
Achtman, M.1
-
3
-
-
33947238287
-
The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific
-
Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, Yooseph S, Wu D, Eisen JA, Hoffman JM, Remington K, Beeson K, Tran B, Smith H, Baden-Tillson H, Stewart C, Thorpe J, Freeman J, Andrews-Pfannkoch C, Venter JE, Li K, Kravitz S, Heidelberg JF, Utterback T, Rogers YH, Falcón LI, Souza V, Bonilla-Rosso G, Eguiarte LE, Karl DM, Sathyendranath S, et al. The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol 2007, 5:398-431.
-
(2007)
PLoS Biol
, vol.5
, pp. 398-431
-
-
Rusch, D.B.1
Halpern, A.L.2
Sutton, G.3
Heidelberg, K.B.4
Williamson, S.5
Yooseph, S.6
Wu, D.7
Eisen, J.A.8
Hoffman, J.M.9
Remington, K.10
Beeson, K.11
Tran, B.12
Smith, H.13
Baden-Tillson, H.14
Stewart, C.15
Thorpe, J.16
Freeman, J.17
Andrews-Pfannkoch, C.18
Venter, J.E.19
Li, K.20
Kravitz, S.21
Heidelberg, J.F.22
Utterback, T.23
Rogers, Y.H.24
Falcón, L.I.25
Souza, V.26
Bonilla-Rosso, G.27
Eguiarte, L.E.28
Karl, D.M.29
Sathyendranath, S.30
more..
-
4
-
-
63849269776
-
Prokaryotic genomes and diversity in surface ocean waters: interrogating the Global Ocean Sampling metagenome
-
10.1128/AEM.02118-08, 2663191, 19201952
-
Biers EJ, Sun S, Howard EC. Prokaryotic genomes and diversity in surface ocean waters: interrogating the Global Ocean Sampling metagenome. Appl Environ Microbiol 2009, 75:2221-2229. 10.1128/AEM.02118-08, 2663191, 19201952.
-
(2009)
Appl Environ Microbiol
, vol.75
, pp. 2221-2229
-
-
Biers, E.J.1
Sun, S.2
Howard, E.C.3
-
5
-
-
34548406920
-
High intraspecific recombination rate in a native population of Candidatus Pelagibacter ubique (SAR11)
-
10.1111/j.1462-2920.2007.01361.x, 17803769
-
Vergin KL, Tripp HJ, Wilhelm LJ, Denver DR, Rappe MS, Giovannoni SJ. High intraspecific recombination rate in a native population of Candidatus Pelagibacter ubique (SAR11). Environ Microbiol 2007, 9:2430-2440. 10.1111/j.1462-2920.2007.01361.x, 17803769.
-
(2007)
Environ Microbiol
, vol.9
, pp. 2430-2440
-
-
Vergin, K.L.1
Tripp, H.J.2
Wilhelm, L.J.3
Denver, D.R.4
Rappe, M.S.5
Giovannoni, S.J.6
-
6
-
-
84874193410
-
Abundant SAR11 viruses in the ocean
-
10.1038/nature11921, 23407494
-
Zhao Y, Temperton B, Thrash JC, Schwalbach MS, Vergin KL, Landry ZC, Ellisman M, Deerinck T, Sullivan MB, Giovannoni SJ. Abundant SAR11 viruses in the ocean. Nature 2013, 494:357-360. 10.1038/nature11921, 23407494.
-
(2013)
Nature
, vol.494
, pp. 357-360
-
-
Zhao, Y.1
Temperton, B.2
Thrash, J.C.3
Schwalbach, M.S.4
Vergin, K.L.5
Landry, Z.C.6
Ellisman, M.7
Deerinck, T.8
Sullivan, M.B.9
Giovannoni, S.J.10
-
7
-
-
84868369211
-
Streamlining and core genome conservation among highly divergent members of the SAR11 clade
-
3448164, 22991429
-
Grote J, Thrash JC, Huggett MJ, Landry ZC, Carini P, Giovannoni SJ, Rappe MS. Streamlining and core genome conservation among highly divergent members of the SAR11 clade. Mbio 2012, 3:e00252-12. 3448164, 22991429.
-
(2012)
Mbio
, vol.3
-
-
Grote, J.1
Thrash, J.C.2
Huggett, M.J.3
Landry, Z.C.4
Carini, P.5
Giovannoni, S.J.6
Rappe, M.S.7
-
8
-
-
27744438187
-
Proteorhodopsin in the ubiquitous marine bacterium SAR11
-
10.1038/nature04032, 16267553
-
Giovannoni SJ, Bibbs L, Cho JC, Stapels MD, Desiderio R, Vergin KL, Rappe MS, Laney S, Wilhelm LJ, Tripp HJ, Mathur EJ, Barofsky DF. Proteorhodopsin in the ubiquitous marine bacterium SAR11. Nature 2005, 438:82-85. 10.1038/nature04032, 16267553.
-
(2005)
Nature
, vol.438
, pp. 82-85
-
-
Giovannoni, S.J.1
Bibbs, L.2
Cho, J.C.3
Stapels, M.D.4
Desiderio, R.5
Vergin, K.L.6
Rappe, M.S.7
Laney, S.8
Wilhelm, L.J.9
Tripp, H.J.10
Mathur, E.J.11
Barofsky, D.F.12
-
9
-
-
84855864414
-
Independent genome reduction and phylogenetic reclassification of the oceanic SAR11 clade
-
10.1093/molbev/msr203, 21900598
-
Viklund J, Ettema TJG, Andersson SGE. Independent genome reduction and phylogenetic reclassification of the oceanic SAR11 clade. Mol Biol Evol 2012, 29:599-615. 10.1093/molbev/msr203, 21900598.
-
(2012)
Mol Biol Evol
, vol.29
, pp. 599-615
-
-
Viklund, J.1
Ettema, T.J.G.2
Andersson, S.G.E.3
-
10
-
-
0037178021
-
Typical freshwater bacteria: an analysis of available 16S rRNA gene sequences from plankton of lakes and rivers
-
Zwart G, Crump BC, Agterveld M, Hagen F, Han SK. Typical freshwater bacteria: an analysis of available 16S rRNA gene sequences from plankton of lakes and rivers. Aquat Microb Ecol 2002, 28:141-155.
-
(2002)
Aquat Microb Ecol
, vol.28
, pp. 141-155
-
-
Zwart, G.1
Crump, B.C.2
Agterveld, M.3
Hagen, F.4
Han, S.K.5
-
11
-
-
44649159553
-
Novel estuarine bacterioplankton in rRNA operon libraries from the Chesapeake Bay
-
Kan J, Evans SE, Chen F, Suzuki MT. Novel estuarine bacterioplankton in rRNA operon libraries from the Chesapeake Bay. Aquat Microb Ecol 2008, 51:55-66.
-
(2008)
Aquat Microb Ecol
, vol.51
, pp. 55-66
-
-
Kan, J.1
Evans, S.E.2
Chen, F.3
Suzuki, M.T.4
-
12
-
-
74549165386
-
Infrequent transitions between saline and fresh waters in one of the most abundant microbial lineages (SAR11)
-
10.1093/molbev/msp239, 19808864
-
Logares R, Brate J, Heinrich F, Shalchian-Tabrizi K, Bertilsson S. Infrequent transitions between saline and fresh waters in one of the most abundant microbial lineages (SAR11). Mol Biol Evol 2010, 27:347-357. 10.1093/molbev/msp239, 19808864.
-
(2010)
Mol Biol Evol
, vol.27
, pp. 347-357
-
-
Logares, R.1
Brate, J.2
Heinrich, F.3
Shalchian-Tabrizi, K.4
Bertilsson, S.5
-
13
-
-
0000450150
-
Bacterial diversity in an arctic lake: a freshwater SAR11 cluster
-
Bahr M, Hobbie JE, Sogin ML. Bacterial diversity in an arctic lake: a freshwater SAR11 cluster. Aquat Microb Ecol 1996, 11:271-277.
-
(1996)
Aquat Microb Ecol
, vol.11
, pp. 271-277
-
-
Bahr, M.1
Hobbie, J.E.2
Sogin, M.L.3
-
14
-
-
0032432257
-
Nearly identical 16S rRNA sequences recovered from lakes in North America and Europe indicate the existence of clades of globally distributed freshwater bacteria
-
10.1016/S0723-2020(98)80067-2, 9924823
-
Zwart G, Hiorns WD, Methe BA, Van Agterveld MP, Huismans R, Nold SC, Zehr JP, Laanbroek HJ. Nearly identical 16S rRNA sequences recovered from lakes in North America and Europe indicate the existence of clades of globally distributed freshwater bacteria. Syst Appl Microbiol 1998, 21:546-556. 10.1016/S0723-2020(98)80067-2, 9924823.
-
(1998)
Syst Appl Microbiol
, vol.21
, pp. 546-556
-
-
Zwart, G.1
Hiorns, W.D.2
Methe, B.A.3
Van Agterveld, M.P.4
Huismans, R.5
Nold, S.C.6
Zehr, J.P.7
Laanbroek, H.J.8
-
15
-
-
79960564713
-
Seasonal bloom dynamics and ecophysiology of the freshwater sister clade of SAR11 bacteria 'that rule the waves' (LD12)
-
10.1038/ismej.2011.8, 3146277, 21412347
-
Salcher MM, Pernthaler J, Posch T. Seasonal bloom dynamics and ecophysiology of the freshwater sister clade of SAR11 bacteria 'that rule the waves' (LD12). ISME J 2011, 5:1242-1252. 10.1038/ismej.2011.8, 3146277, 21412347.
-
(2011)
ISME J
, vol.5
, pp. 1242-1252
-
-
Salcher, M.M.1
Pernthaler, J.2
Posch, T.3
-
16
-
-
69749086719
-
Infrequent marine-freshwater transitions in the microbial world
-
10.1016/j.tim.2009.05.010, 19726194
-
Logares R, Brate J, Bertilsson S, Clasen JL, Shalchian-Tabrizi K, Rengefors K. Infrequent marine-freshwater transitions in the microbial world. Trends Microbiol 2009, 17:414-422. 10.1016/j.tim.2009.05.010, 19726194.
-
(2009)
Trends Microbiol
, vol.17
, pp. 414-422
-
-
Logares, R.1
Brate, J.2
Bertilsson, S.3
Clasen, J.L.4
Shalchian-Tabrizi, K.5
Rengefors, K.6
-
17
-
-
84868098266
-
Single cell genomics: an individual look at microbes
-
10.1016/j.mib.2012.09.001, 23026140
-
Stepanauskas R. Single cell genomics: an individual look at microbes. Curr Opin Microbiol 2012, 15:613-620. 10.1016/j.mib.2012.09.001, 23026140.
-
(2012)
Curr Opin Microbiol
, vol.15
, pp. 613-620
-
-
Stepanauskas, R.1
-
18
-
-
84864394611
-
Genomic sequencing of uncultured microorganisms from single cells
-
10.1038/nrmicro2857, 22890147
-
Lasken RS. Genomic sequencing of uncultured microorganisms from single cells. Nat Rev Microbiol 2012, 10:631-640. 10.1038/nrmicro2857, 22890147.
-
(2012)
Nat Rev Microbiol
, vol.10
, pp. 631-640
-
-
Lasken, R.S.1
-
19
-
-
84355163060
-
High-throughput single-cell sequencing identifies photoheterotrophs and chemoautotrophs in freshwater bacterioplankton
-
10.1038/ismej.2011.84, 3246240, 21716306
-
Martinez-Garcia M, Swan BK, Poulton NJ, Gomez ML, Masland D, Sieracki ME, Stepanauskas R. High-throughput single-cell sequencing identifies photoheterotrophs and chemoautotrophs in freshwater bacterioplankton. ISME J 2012, 6:113-123. 10.1038/ismej.2011.84, 3246240, 21716306.
-
(2012)
ISME J
, vol.6
, pp. 113-123
-
-
Martinez-Garcia, M.1
Swan, B.K.2
Poulton, N.J.3
Gomez, M.L.4
Masland, D.5
Sieracki, M.E.6
Stepanauskas, R.7
-
20
-
-
25144481245
-
Temporal and spatial response of bacterioplankton lineages to annual convective overturn at the Bermuda Atlantic time-series study site
-
Morris RM, Vergin KL, Cho JC, Rappe MS, Carlson CA, Giovannoni SJ. Temporal and spatial response of bacterioplankton lineages to annual convective overturn at the Bermuda Atlantic time-series study site. Limnol Oceanogr 2005, 50:1687-1696.
-
(2005)
Limnol Oceanogr
, vol.50
, pp. 1687-1696
-
-
Morris, R.M.1
Vergin, K.L.2
Cho, J.C.3
Rappe, M.S.4
Carlson, C.A.5
Giovannoni, S.J.6
-
21
-
-
73449098993
-
Inference of microbial recombination rates from metagenomic data
-
10.1371/journal.pgen.1000674, 2745702, 19798447
-
Johnson PL, Slatkin M. Inference of microbial recombination rates from metagenomic data. PLoS Genet 2009, 5:e1000674. 10.1371/journal.pgen.1000674, 2745702, 19798447.
-
(2009)
PLoS Genet
, vol.5
-
-
Johnson, P.L.1
Slatkin, M.2
-
22
-
-
48349124258
-
High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi
-
10.1038/ng.195, 2652037, 18660809
-
Holt KE, Parkhill J, Mazzoni CJ, Roumagnac P, Weill F-X, Goodhead I, Rance R, Baker S, Maskell DJ, Wain J, Dolecek C, Achtman M, Dougan G. High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi. Nat Genet 2008, 40:987-993. 10.1038/ng.195, 2652037, 18660809.
-
(2008)
Nat Genet
, vol.40
, pp. 987-993
-
-
Holt, K.E.1
Parkhill, J.2
Mazzoni, C.J.3
Roumagnac, P.4
Weill, F.-X.5
Goodhead, I.6
Rance, R.7
Baker, S.8
Maskell, D.J.9
Wain, J.10
Dolecek, C.11
Achtman, M.12
Dougan, G.13
-
23
-
-
0033598784
-
Yersinia pestis, the cause of plague, is a recently emerged clone of Yersinia pseudotuberculosis
-
10.1073/pnas.96.24.14043, 24187, 10570195
-
Achtman M, Zurth K, Morelli C, Torrea G, Guiyoule A, Carniel E. Yersinia pestis, the cause of plague, is a recently emerged clone of Yersinia pseudotuberculosis. Proc Natl Acad Sci U S A 1999, 96:14043-14048. 10.1073/pnas.96.24.14043, 24187, 10570195.
-
(1999)
Proc Natl Acad Sci U S A
, vol.96
, pp. 14043-14048
-
-
Achtman, M.1
Zurth, K.2
Morelli, C.3
Torrea, G.4
Guiyoule, A.5
Carniel, E.6
-
24
-
-
59649113973
-
Evolution of pathogenicity in the Bacillus cereus group
-
10.1016/j.syapm.2009.01.001, 19200684
-
Didelot X, Barker M, Falush D, Priest FG. Evolution of pathogenicity in the Bacillus cereus group. Syst Appl Microbiol 2009, 32:81-90. 10.1016/j.syapm.2009.01.001, 19200684.
-
(2009)
Syst Appl Microbiol
, vol.32
, pp. 81-90
-
-
Didelot, X.1
Barker, M.2
Falush, D.3
Priest, F.G.4
-
25
-
-
0038628890
-
Multilocus sequence typing and evolutionary relationships among the causative agents of melioidosis and glanders, Burkholderia pseudomallei and Burkholderia mallei
-
10.1128/JCM.41.5.2068-2079.2003, 154742, 12734250
-
Godoy D, Randle G, Simpson AJ, Aanensen DM, Pitt TL, Kinoshita R, Spratt BG. Multilocus sequence typing and evolutionary relationships among the causative agents of melioidosis and glanders, Burkholderia pseudomallei and Burkholderia mallei. J Clin Microbiol 2003, 41:2068-2079. 10.1128/JCM.41.5.2068-2079.2003, 154742, 12734250.
-
(2003)
J Clin Microbiol
, vol.41
, pp. 2068-2079
-
-
Godoy, D.1
Randle, G.2
Simpson, A.J.3
Aanensen, D.M.4
Pitt, T.L.5
Kinoshita, R.6
Spratt, B.G.7
-
26
-
-
77952841173
-
Human T cell epitopes of Mycobacterium tuberculosis are evolutionarily hyperconserved
-
10.1038/ng.590, 2883744,2883744, 20495566
-
Comas I, Chakravartti J, Small PM, Galagan J, Niemann S, Kremer K, Ernst JD, Gagneux S. Human T cell epitopes of Mycobacterium tuberculosis are evolutionarily hyperconserved. Nat Genet 2010, 42:498-503. 10.1038/ng.590, 2883744,2883744, 20495566.
-
(2010)
Nat Genet
, vol.42
, pp. 498-503
-
-
Comas, I.1
Chakravartti, J.2
Small, P.M.3
Galagan, J.4
Niemann, S.5
Kremer, K.6
Ernst, J.D.7
Gagneux, S.8
-
27
-
-
84875835323
-
Genetic diversity of Bartonella quintana in macaques suggests zoonotic origin of trench fever
-
10.1111/mec.12261, 23517327
-
Li H, Bai J-Y, Wang L-Y, Zeng L, Shi Y-S, Qiu Z-L, Ye H-H, Zhang X-F, Lu Q-B, Kosoy M, Liu W, Cao WC. Genetic diversity of Bartonella quintana in macaques suggests zoonotic origin of trench fever. Mol Ecol 2013, 22:2118-2127. 10.1111/mec.12261, 23517327.
-
(2013)
Mol Ecol
, vol.22
, pp. 2118-2127
-
-
Li, H.1
Bai, J.-Y.2
Wang, L.-Y.3
Zeng, L.4
Shi, Y.-S.5
Qiu, Z.-L.6
Ye, H.-H.7
Zhang, X.-F.8
Lu, Q.-B.9
Kosoy, M.10
Liu, W.11
Cao, W.C.12
-
28
-
-
84856652357
-
Insights from genomic comparisons of genetically monomorphic bacterial pathogens
-
Achtman M. Insights from genomic comparisons of genetically monomorphic bacterial pathogens. Phil Trans R Soc Lond B Biol Sci 2012, 367:860-867.
-
(2012)
Phil Trans R Soc Lond B Biol Sci
, vol.367
, pp. 860-867
-
-
Achtman, M.1
-
29
-
-
70350180460
-
Explaining microbial population genomics through phage predation
-
10.1038/nrmicro2235, 19834481
-
Rodriguez-Valera F, Martin-Cuadrado A-B, Rodriguez-Brito B, Pasic L, Thingstad TF, Rohwer F, Mira A. Explaining microbial population genomics through phage predation. Nat Rev Microbiol 2009, 7:828-836. 10.1038/nrmicro2235, 19834481.
-
(2009)
Nat Rev Microbiol
, vol.7
, pp. 828-836
-
-
Rodriguez-Valera, F.1
Martin-Cuadrado, A.-B.2
Rodriguez-Brito, B.3
Pasic, L.4
Thingstad, T.F.5
Rohwer, F.6
Mira, A.7
-
30
-
-
84872011667
-
DOE Joint Genome Institute
-
DOE Joint Genome Institute. http://www.jgi.doe.gov/.
-
-
-
-
31
-
-
43149115851
-
Velvet: algorithms for de novo short read assembly using de Bruijn graphs
-
10.1101/gr.074492.107, 2336801, 18349386
-
Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008, 18:821-829. 10.1101/gr.074492.107, 2336801, 18349386.
-
(2008)
Genome Res
, vol.18
, pp. 821-829
-
-
Zerbino, D.R.1
Birney, E.2
-
32
-
-
79952178131
-
High-quality draft assemblies of mammalian genomes from massively parallel sequence data
-
10.1073/pnas.1017351108, 3029755, 21187386
-
Gnerre S, MacCallum I, Przybylski D, Ribeiro FJ, Burton JN, Walker BJ, Sharpe T, Hall G, Shea TP, Sykes S, Berlin AM, Aird D, Costello M, Daza R, Williams L, Nicol R, Gnirke A, Nusbaum C, Lander ES, Jaffe DB. High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci U S A 2011, 108:1513-1518. 10.1073/pnas.1017351108, 3029755, 21187386.
-
(2011)
Proc Natl Acad Sci U S A
, vol.108
, pp. 1513-1518
-
-
Gnerre, S.1
MacCallum, I.2
Przybylski, D.3
Ribeiro, F.J.4
Burton, J.N.5
Walker, B.J.6
Sharpe, T.7
Hall, G.8
Shea, T.P.9
Sykes, S.10
Berlin, A.M.11
Aird, D.12
Costello, M.13
Daza, R.14
Williams, L.15
Nicol, R.16
Gnirke, A.17
Nusbaum, C.18
Lander, E.S.19
Jaffe, D.B.20
more..
-
33
-
-
0141519279
-
OrthoMCL: Identification of ortholog groups for eukaryotic genomes
-
10.1101/gr.1224503, 403725, 12952885
-
Li L, Stoeckert CJ, Roos DS. OrthoMCL: Identification of ortholog groups for eukaryotic genomes. Genome Res 2003, 13:2178-2189. 10.1101/gr.1224503, 403725, 12952885.
-
(2003)
Genome Res
, vol.13
, pp. 2178-2189
-
-
Li, L.1
Stoeckert, C.J.2
Roos, D.S.3
-
34
-
-
13744252890
-
MAFFT version 5: improvement in accuracy of multiple sequence alignment
-
10.1093/nar/gki198, 548345, 15661851
-
Katoh K, Kuma K, Toh H, Miyata T. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res 2005, 33:511-518. 10.1093/nar/gki198, 548345, 15661851.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 511-518
-
-
Katoh, K.1
Kuma, K.2
Toh, H.3
Miyata, T.4
-
35
-
-
0034043778
-
Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis
-
10.1093/oxfordjournals.molbev.a026334, 10742046
-
Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000, 17:540-552. 10.1093/oxfordjournals.molbev.a026334, 10742046.
-
(2000)
Mol Biol Evol
, vol.17
, pp. 540-552
-
-
Castresana, J.1
-
36
-
-
79954529507
-
ProtTest 3: fast selection of best-fit models of protein evolution
-
10.1093/bioinformatics/btr088, 21335321
-
Darriba D, Taboada GL, Doallo R, Posada D. ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics 2011, 27:1164-1165. 10.1093/bioinformatics/btr088, 21335321.
-
(2011)
Bioinformatics
, vol.27
, pp. 1164-1165
-
-
Darriba, D.1
Taboada, G.L.2
Doallo, R.3
Posada, D.4
-
37
-
-
33750403801
-
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
-
10.1093/bioinformatics/btl446, 16928733
-
Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006, 22:2688-2690. 10.1093/bioinformatics/btl446, 16928733.
-
(2006)
Bioinformatics
, vol.22
, pp. 2688-2690
-
-
Stamatakis, A.1
-
38
-
-
77954272855
-
TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations
-
10.1093/nar/gkq291, 2896173, 20435676
-
Abascal F, Zardoya R, Telford MJ. TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations. Nucleic Acids Res 2010, 38:W7-W13. 10.1093/nar/gkq291, 2896173, 20435676.
-
(2010)
Nucleic Acids Res
, vol.38
-
-
Abascal, F.1
Zardoya, R.2
Telford, M.J.3
-
39
-
-
0033979433
-
Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models
-
10.1093/oxfordjournals.molbev.a026236, 10666704
-
Yang ZH, Nielsen R. Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol Biol Evol 2000, 17:32-43. 10.1093/oxfordjournals.molbev.a026236, 10666704.
-
(2000)
Mol Biol Evol
, vol.17
, pp. 32-43
-
-
Yang, Z.H.1
Nielsen, R.2
-
40
-
-
34547803197
-
PAML 4: Phylogenetic analysis by maximum likelihood
-
10.1093/molbev/msm088, 17483113
-
Yang Z. PAML 4: Phylogenetic analysis by maximum likelihood. Mol Biol Evol 2007, 24:1586-1591. 10.1093/molbev/msm088, 17483113.
-
(2007)
Mol Biol Evol
, vol.24
, pp. 1586-1591
-
-
Yang, Z.1
-
41
-
-
77956193448
-
ProgressiveMauve: multiple genome alignment with gene gain, loss and rearrangement
-
10.1371/journal.pone.0010209, 2855710, 20419134
-
Darling AE, Mau B, Perna NT. progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One 2010, 5:e10209. 10.1371/journal.pone.0010209, 2855710, 20419134.
-
(2010)
PLoS One
, vol.5
-
-
Darling, A.E.1
Mau, B.2
Perna, N.T.3
-
42
-
-
34249027580
-
Inference of bacterial microevolution using multilocus sequence data
-
1840087, 17151252
-
Didelot X, Falush D. Inference of bacterial microevolution using multilocus sequence data. Genetics 2007, 175:1251-1266. 1840087, 17151252.
-
(2007)
Genetics
, vol.175
, pp. 1251-1266
-
-
Didelot, X.1
Falush, D.2
-
43
-
-
75149150388
-
TreeGraph 2: combining and visualizing evidence from different phylogenetic analyses
-
10.1186/1471-2105-11-7, 2806359, 20051126
-
Stoever BC, Mueller KF. TreeGraph 2: combining and visualizing evidence from different phylogenetic analyses. BMC Bioinformatics 2010, 11:7. 10.1186/1471-2105-11-7, 2806359, 20051126.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 7
-
-
Stoever, B.C.1
Mueller, K.F.2
-
44
-
-
80055082271
-
Accelerated profile HMM searches
-
Eddy SR. Accelerated profile HMM searches. PLoS Comp Biol 2011, 7:e1002195.
-
(2011)
PLoS Comp Biol
, vol.7
-
-
Eddy, S.R.1
-
45
-
-
2942538300
-
Versatile and open software for comparing large genomes
-
10.1186/gb-2004-5-2-r12, 395750, 14759262
-
Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL. Versatile and open software for comparing large genomes. Genome Biol 2004, 5:R12. 10.1186/gb-2004-5-2-r12, 395750, 14759262.
-
(2004)
Genome Biol
, vol.5
-
-
Kurtz, S.1
Phillippy, A.2
Delcher, A.L.3
Smoot, M.4
Shumway, M.5
Antonescu, C.6
Salzberg, S.L.7
-
46
-
-
45949107473
-
Recent developments in the MAFFT multiple sequence alignment program
-
10.1093/bib/bbn013, 18372315
-
Katoh K, Toh H. Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform 2008, 9:286-298. 10.1093/bib/bbn013, 18372315.
-
(2008)
Brief Bioinform
, vol.9
, pp. 286-298
-
-
Katoh, K.1
Toh, H.2
-
47
-
-
84861898310
-
IMG: the Integrated Microbial Genomes database and comparative analysis system
-
10.1093/nar/gkr1044, 3245086, 22194640
-
Markowitz VM, Chen IM, Palaniappan K, Chu K, Szeto E, Grechkin Y, Ratner A, Jacob B, Huang J, Williams P, Huntemann M, Anderson I, Mavromatis K, Ivanova NN, Kyrpides NC. IMG: the Integrated Microbial Genomes database and comparative analysis system. Nucleic Acids Res 2012, 40:D115-D122. 10.1093/nar/gkr1044, 3245086, 22194640.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Markowitz, V.M.1
Chen, I.M.2
Palaniappan, K.3
Chu, K.4
Szeto, E.5
Grechkin, Y.6
Ratner, A.7
Jacob, B.8
Huang, J.9
Williams, P.10
Huntemann, M.11
Anderson, I.12
Mavromatis, K.13
Ivanova, N.N.14
Kyrpides, N.C.15
-
48
-
-
77956519355
-
GenoPlotR: comparative gene and genome visualization in R
-
10.1093/bioinformatics/btq413, 2935412, 20624783
-
Guy L, Kultima JR, Andersson SGE. genoPlotR: comparative gene and genome visualization in R. Bioinformatics 2010, 26:2334-2335. 10.1093/bioinformatics/btq413, 2935412, 20624783.
-
(2010)
Bioinformatics
, vol.26
, pp. 2334-2335
-
-
Guy, L.1
Kultima, J.R.2
Andersson, S.G.E.3
|