[http://​www.​repeatmasker.​org] 53. House CH, Runnegar B, Fitz-Gibbon ST: Geobiological analysis using whole genome-based tree building applied to the bacteria, archaea, and eukarya. Geobiology 2003, 1:15–26.CrossRef 54. Huse SM, Huber JA, Morrison HG, Sogin ML, Welch DM: Accuracy and quality of massively parallel DNA pyrosequencing. Genome learn more Biol 2007,8(7):R143.PubMedCrossRef 55. Kunin V, Engelbrektson A, Ochman H, Hugenholtz P: Wrinkles in the rare biosphere: pyrosequencing

errors can lead to artificial inflation of diversity estimates. Environ Microbiol 2010,12(1):118–123.PubMedCrossRef 56. Niu B, Fu L, Sun S, Li W: Artificial and natural duplicates in pyrosequencing reads of metagenomic data. BMC Bioinforma 2010,11(1):187.CrossRef 57. Gilbert MTP, Binladen J, Miller W, Wiuf C, Willerslev E, Poinar H, Carlson JE, Leebens-Mack JH, Schuster SC: Recharacterization of ancient DNA miscoding lesions: insights in the era of sequencing-by-synthesis. Nucleic Acids KPT 330 Res 2007,35(1):1–10.PubMedCrossRef 58. Quince C, Lanzen A, Davenport RJ, Turnbaugh PJ: Removing noise from pyrosequenced amplicons. BMC Bioinforma 2011, 12:38.CrossRef 59. Kitts CL: Terminal restriction fragment patterns: a tool for comparing microbial communities and assessing community dynamics. Curr Issues Intest Microbiol 2001,2(1):17–25.PubMed 60. Bukovska P, Jelinkova M, Hrselova H, Sykorova Z, Gryndler M: Terminal restriction fragment LXH254 ic50 length measurement errors are affected mainly

by fragment length, G plus C nucleotide content and secondary structure melting point. J Microbiol Methods 2010,82(3):223–228.PubMedCrossRef 61. Kaplan CW, Kitts CL: Variation between observed and true terminal restriction fragment length is dependent on true TRF

length and purine content. J Microbiol Methods 2003,54(1):121–125.PubMedCrossRef 62. Osborn AM, Moore ERB, Timmis KN: An evaluation of terminal-restriction fragment length polymorphism (T-RFLP) analysis for the study of microbial community structure and dynamics. Environ Microbiol 2000,2(1):39–50.PubMedCrossRef 63. Clement BG, Kehl LE, DeBord KL, Kitts CL: Terminal restriction fragment patterns (TRFPs), a rapid, PCR-based method for the comparison of complex bacterial communities. J Microbiol Methods 1998,31(3):135–142.CrossRef 64. Egert M, Friedrich MW: Formation of pseudo-terminal Selleckchem Lonafarnib restriction fragments, a PCR-related bias affecting terminal restriction fragment length polymorphism analysis of microbial community structure. Appl Environ Microbiol 2003,69(5):2555–2562.PubMedCrossRef 65. Pilloni G, von Netzer F, Engel M, Lueders T: Electron acceptor-dependent identification of key anaerobic toluene degraders at a tar-oil-contaminated aquifer by pyro-SIP. FEMS Microbiol Ecol 2011,78(1):165–175.PubMedCrossRef 66. Meyer F, Paarmann D, D′Souza M, Olson R, Glass EM, Kubal M, Paczian T, Rodriguez A, Stevens R, Wilke A, et al.: The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes.