Phylogeny of Competence 26. Bruen TC, Philippe H, Bryant D (2006) A simple and robust statistical test for detecting the presence of recombination. Genetics 172: 2665–2681. 27. Huson DH (1998) SplitsTree: A program for analyzing and visualizing evolutionary data. Bioinformatics 14: 68–73. 28. Huson DH, Bryant D (2006) Application of phylogenetic networks in evolutionary studies. Mol Biol Evol 23: 254–267. 29. Martin DP, Williamson C, Posada D (2005) RDP2: recombination detection and analysis from sequence alignments. Bioinformatics 21: 260–262. 30. Huelsenbeck JP, Ronquist F (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754–755. 31. Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572–1574. 32. Ane C, Larget B, Baum DA, Smith SD, Rokas A (2007) Bayesian estimation of concordance among gene trees. Mol Biol Evol 24: 412–426. 33. Didelot X, Falush D (2007) Inference of bacterial microevolution using multilocus sequence data. Genetics 175: 1251–1266. 34. Maddison WP, Maddison DR (2008) Mesquite: a modular system for evolutionary analysis. Version 2.5 http://mesquiteproject.org. 35. Gwinn ML, Ramanathan R, Smith HO, Tomb JF (1998) A new transformation-deficient mutant of Haemophilus influenzae Rd with normal DNA uptake. J Bacteriol 180: 746–748. 36. Redfield RJ, Findlay WA, Bosse J, Kroll JS, Cameron AD, et al. (2006) Evolution of competence and DNA uptake specificity in the Pasteurellaceae. BMC Evol Biol 6: 82. 37. Barabote RD, Saier MH Jr (2005) Comparative genomic analyses of the bacterial phosphotransferase system. Microbiol Mol Biol Rev 69: 608–634. 38. Darling AC, Mau B, Blattner FR, Perna NT (2004) Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res 14: 1394–1403. 39. Darling AE, Treangen TJ, Messeguer X, Perna NT (2007) Analyzing patterns of microbial evolution using the mauve genome alignment system. Methods Mol Biol 396: 135–152. 40. Maughan H, Sinha S, Wilson L, Redfield RJ (2008) Competence, DNA uptake, and Transformation in Pasteurellaceae. In: Kuhnert P, Christensen H, eds. Pasteurellaceae: Biology, Genomics, and Molecular Aspects Horizon Scientific Press. 41. Posada D, Crandall KA (1998) MODELTEST: testing the model of DNA substitution. Bioinformatics 14: 817–818. 42. Martin DP, Rybicki E (2000) RDP: detection of recombination amongst aligned sequences. Bioinformatics 16: 562–563. 43. Maynard Smith J (1992) Analyzing the mosaic structure of genes. Journal of Molecular Evolution 34: 126–129. 44. Posada D, Crandall KA (2001) Evaluation of methods for detecting recombination from DNA sequences: computer simulations. Proc Natl Acad Sci U S A 98: 13757–13762. 45. Salminen MO, Carr JK, Burke DS, McCutchan FE (1995) Identification of breakpoints in intergenotypic recombinants of HIV type 1 by bootscanning. AIDS Res Hum Retroviruses 11: 1423–1425. 46. Gibbs MJ, Armstrong JS, Gibbs AJ (2000) Sister-scanning: a Monte Carlo procedure for assessing signals in recombinant sequences. Bioinformatics 16: 573–582. 47. Boni MF, Posada D, Feldman MW (2007) An exact nonparametric method for inferring mosaic structure in sequence triplets. Genetics 176: 1035–1047. PLoS ONE | www.plosone.org 13 June 2009 | Volume 4 | Issue 6 | e5854