Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties learn more and weight matrix PD-1/PD-L1 inhibitor clinical trial choice. Nucleic Acids Res 1994,22(22):4673–4680.PubMedCrossRef 32. Wernersson R, Pedersen A: RevTrans: Multiple alignment of coding DNA from aligned amino acid sequences. Nucleic Acids Res 2003,31(13):3537.PubMedCrossRef 33. Librado P, Rozas J: DnaSP v5:

A software for comprehensive analysis of DNA polymorphism data. Bioinformatics 2009,25(11):1451.PubMedCrossRef 34. Kumar S, Nei M, Dudley J, Tamura K: MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform 2008,9(4):299–306.PubMedCrossRef 35. Nei

M, Gojobori T: Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 1986,3(5):418.PubMed 36. Simpson E: Measurement of diversity. Nature 1949,163(4148):688.CrossRef 37. Gomes J, Nunes A, Bruno W, Borrego M, Florindo C, Dean D: Polymorphisms in the nine polymorphic membrane proteins of Chlamydia trachomatis across all serovars: Evidence for serovar Da recombination and correlation with tissue tropism. J Bacteriol 2006,188(1):275.PubMedCrossRef 38. Nunes A, Nogueira P, Borrego M, Gomes J: Chlamydia trachomatis diversity viewed as a tissue-specific coevolutionary arms race. Genome Biol 2008,9(10):110–123.CrossRef 39. Greub G, Collyn F, Guy L, Roten C: A genomic island present along the bacterial chromosome of the Parachlamydiaceae UWE 25, an obligate amoebal endosymbiont, encodes a potentially functional F-like conjugative DNA transfer selleck chemicals system. BMC Microbiol 2004,4(1):48.PubMedCrossRef 40. Eugster M, Roten C, Greub G: Analyses of six homologous proteins of Protochlamydia amoebophila UWE 25 encoded by large GC-rich genes: A model of evolution

and concatenation of leucine-rich repeats. BMC Evol Biol 2007,7(1):231.PubMedCrossRef 41. Woese CR: Bacterial evolution. Microbiol Mol Biol Rev 1987,51(2):221–271. 42. Watve M, Gangal R: Problems in measuring bacterial diversity and a possible solution. Appl Environ Microbiol 1996,62(11):4299.PubMed 43. Mills A, Wassel R: Aspects of diversity measurement for microbial communities. Appl Environ Microbiol C-X-C chemokine receptor type 7 (CXCR-7) 1980,40(3):578.PubMed 44. Ikryannikova LN, Shkarupeta MM, Shitikov EA, Il’ina EN, Govorun VM: Comparative evaluation of new typing schemes for urogenital Chlamydia trachomatis isolates. FEMS Immunol Med Microbiol 2010,6(2):144–156. 45. Posada D, Crandall KA: Modeltest: Testing the model of DNA substitution. Bioinformatics 1998,14(9):817.PubMedCrossRef 46. Timms P, Eaves FW, Girjes AA, Lavin MF: Comparison of Chlamydia psittaci isolates by restriction endonuclease and DNA probe analyses. Infect Immun 1988,56(1):287–290.PubMed 47. Martin D: Recombination detection and analysis using RDP3. Methods Mol Biol 2009, 537:185–205.PubMedCrossRef 48.