Appl Environ Microbiol 2008, 74:6987–6996.PubMedCrossRef 45. Edgar RC: MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004, 32:1792–1797.PubMedCrossRef 46. Posada D, Crandall KA: MODELTEST: testing the model of DNA substitution.

Bioinformatics 1998, 14:817–818.PubMedCrossRef 47. Guindon S, Delsuc F, Dufayard JF, Gascuel O: Estimating maximum likelihood this website phylogenies with PhyML. Methods Mol Biol 2009, 537:113–137.PubMedCrossRef 48. Hirsch PR, Van Montagu M, Johnston AWB, Brewin NJ, Schell J: Physical identification of bacteriocinogenic, nodulation and other plasmids in strains of R. leguminosarum . J Gen Microbiol 1980, 120:403–412. 49. Ewing B, Hillier L, Wendl MC, Green P: Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 1998, 8:175–185.PubMed 50. Ewing B, Green P: Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 1998, 8:186–194.PubMed 51. Gordon D, Abajian C, Green P: Consed: a graphical tool Selleck MS275 for sequence finishing. Genome Res 1998, 8:195–202.PubMed 52. Delcher AL, Harmon D, Kasif S, White O, Evofosfamide Salzberg SL:

Improved microbial gene identification with GLIMMER. Nucleic Acids Res 1999, 27:4636–4641.PubMedCrossRef 53. Salzberg SL, Delcher AL, Kasif S, White O: Microbial gene identification using interpolated Markov models. Nucleic Acids Res 1998, 26:544–548.PubMedCrossRef 54. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl Acids Res 1997, 25:3389–3402.PubMedCrossRef 55. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL: GenBank. Nucleic Acids Res 2005, 33:D34-D38.PubMedCrossRef 56. Apweiler RT, Attwood K, Bairoch A, Bateman A, Birney E, Biswas M, Cerutti P, Corpet F, Croning MDR, Durbin R, Falquet L, Fleischmann W, Gouzy J, Hermjakob H, Hulo N, Kahn D, Kanapin A, Karavidopoulou Y, Lopez R, Marx B, Mulder NJ, Oinn TM, Pagni M, Servant F, Sigrist CJA, Zdobnov EM: The InterPro database,

an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res 2001, 29:37–40.PubMedCrossRef 57. Rutherford K, Parkhill J, Crook J, Horsnell TT, Rice Rajandream MA, Casein kinase 1 Barrell B: Artemis: sequence visualization and annotation. Bioinformatics 2000, 16:944–945.PubMedCrossRef 58. Quinto C, de la Vega, Flores HM, Fernández L, Ballado T, Soberón GG, Palacios R: Reiteration of nitrogen fixation gene sequences in Rhizobium phaseoli . Nature 1982, 299:724–728.CrossRef 59. Sambrook J, Fritsch EF, Maniatis T: Molecular cloning: a laboratory manual. Cold Spring Harbor, Cold Spring Harbor Laboratory Press; 1989. 60. Simon R: High frequency mobilization of gram-negative bacterial replicons by the in vitro constructed Tn5-Mob transposon. Mol Gen Genet 1984, 196:413–420.