Selection, Concatenation and Fusion of Sequences

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Workflow of SCaFoS usage

Main steps to use SCaFoS (steps 1, 3 and 5 are done by SCaFoS)
  1. SPECIES PRESENCE: lists all species included into the files of aligned sequences followed by their representation across genes
  2. Define the selected species and define species OTUs
  3. FILE SELECTION: creates files containing only selected species
  4. Discard ambiguously aligned positions (displayed in dark color) with a tool such as GBlocks. Make phylogenetic trees (using PHYML or PAUP for example)
  5. ASSEMBLING DATASETS: Selects sequences and makes chimeras according to an OTU file and default sequence files: creation of files including chimera and selected sequences (A) and creation of concatenated file (B) for super-tree and super-matrix use respectively. Creation of chimera is displayed in green; selected sequences are in blue; eliminated sequences are boxed in dark color and displayed in gray in the trees.
In the last step, four typical cases are represented:

(i) creation of a chimera (Sp5 and Sp6, orange file),
(ii) elimination of a too short sequence (Sp3, red file),
(iii) selection of less divergent sequence within an OTU (Sp6 and Sp5, red file) and
(iv) elimination of potential paralogous sequences (Sp3 and Sp7, purple file).
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Hervé PHILIPPE's Lab