Flowchart of sequences selection and construction of chimera for an OTU in a given gene. For each OTU of each gene, SCaFoS selects the sequence that best represents the OTU. See text for a detailed description of the process. Three thresholds (empty blue rhombus) with default or user specific values are important: (i) the maximal percentage of characters present with respect to the longest sequence to keep a sequence, (ii) the minimal percentage of characters present with respect to the longest sequence to consider a sequence as complete and (iii) the maximum in-OTU/out-OTU distances ratio (see text) to keep an OTU. The user should select if he/she desires to create or not chimerical sequences and chose among the different sequence selection criteria (filled blue rhombus). If the selection criterion is the sequence size, no other options should be checked. If the selection criterion is the evolutionary rate of the sequences, the user must chose between a fully automatic or a semi-automatic choice of sequences and specify if he/she desires to use a previously defined selection.