Simplified flowchart depicting FcC-G implemented options. Possible alignment input file formats, which can be processed individually or in combination, are listed in the top section. The hierarchical flow of possible processing options is depicted by the direction of the arrow in the middle of the figure. Processing options can be combined following the flow direction. For processing chains that contradict this flow direction, FcC-G has to be run twice. Possible output files of FcC-G are depicted on the bottom section. The content of output files depends on the chosen processing options and the type of sequences in given input file alignments. A more detailed description of possible FcC-G input/output files, implemented processing options, and examples of complex process chains are discussed in the FcC-G manual.