Main steps to use SCaFoS. Steps 1, 3 and 5 are done by SCaFoS: 1. SPECIES PRESENCE: listing of all species present in the files of aligned sequences followed by their frequency of presence and, if desired, classified into taxonomic groups (specified by TaxGp in the figure). 2. Definition by the user of the species to be selected and their respective OTUs 3. FILE SELECTION: creation of files containing only the selected species 4. Discarding ambiguously aligned positions (displayed in dark colour) with a tool such as GBlocks ; making phylogenetic trees (using PHYML  or PAUP  for example) 5. DATASETS ASSEMBLING: selection of sequences and chimera construction according to an OTU file and default sequence files: creation of single gene files including chimeras and selected sequences and creation of concatenated files for super-tree and super-matrix approaches respectively. In the last step, three typical cases are represented: (i) construction of a chimera (OTU5) in the orange file, (ii) selection of the less divergent sequence within an OTU (Sp6 in OTU5) and elimination of a short sequence (Sp31) in the red file and (iii) elimination of potential paralogous sequences by the user (Sp31 and Sp71) in the purple file. Eliminated sequences are drawn in grey. The corresponding default sequences files are displayed under their respective sequence files.