cosmos [OutputDirectory] [InputDirectory]
OutputDirectory and InputDirectory are optional arguments to tell the program where to place output files and where to search for input files. If only one directory is specified, it is taken to be the output directory. The system is configured via the input files params.ini, genetic_code.ini and ancestor.ini, described in Section A.5. If either the input or output directory is unspecified when the program is started, the current working directory will be used by default.