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Genedoc: a tool for editing and annoting multiple sequence alignments. 1997. 71. Huber T, not Faulkner G, Hugenholtz P: Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics Applications Note 2004., 20: 72. Cole JR, Chai B, Farris RJ, Wang Q, Kulam SA, McGarrell DM, Garrity GM, Tiedje JM: The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis. Nucl AC Res 2005, (33 Database):D294–296. Authors’ contributions All authors read and approved the final manuscript. SJ was the responsible of this study and participated in the experimental design. LB realised all analyses except for the flagellate counting and phylotype analysis. TP made the cloning-sequencing analysis of the selected DGGE bands. ID participated to the experimental design and realised the flagellate counting. Writing was mainly done by LB, helped and corrected by ID and SJ. Authors’ MK5108 cell line information LB and TP have been PhD students, working in the BioFEEL group between 2007 and early 2011. ID and SJ have obtained permanent positions since 2000, as research scientists.