Likewise, the first codon position is expected to evolve slightly faster than the second. The distribution is scaled such that the mean rate for all the sites is 1 but the user must supply a parameter which describes its shape. The format for the output files was chosen for its simplicity and for the wide range of programs that use it. The general format is a minus sign followed by a code letter. If required, the values of any parameters come after the code, separated from both code and each other with either a comma or a space.
Some options act like switches and require no parameters.
The case of the options is ignored. The first two models are quite similar but not identical. They both require a transition transversion ratio and relative base frequencies as parameters. If no model is specified, the default is F84 which is computationally simpler. This option allows the user to set the length in nucleotides that each simulated sequence should be.