Recodon simulates coding DNA sequences with recombination, migration and demographic periods. Coalescent simulations of codon models with recombination, migration and demography.

The input of the program consists of a series of arguments and parameter values that can be entered in the command line or, more conveniently, specified in a text file called "parameters" that should be located in the same directory as the executable.
These arguments include the parameter values used in the simulations and several printing options that control the amount of information that is sent to the console or output files.

In Mac systems, the command line is provided by the Terminal, while in Windows, this is provided by the windows console or command prompt. If the user specifies any argument in the command line, Recodon will use the values specified for those parameters, and default values for the parameters not included in the command line.

If no argument is specified, the program will look for the text file "parameters" in the same directory as the executable.

By default, the most recent common ancestor (MRCA) sequence is simulated according to the nucleotide frequencies. However, the user can specify its own MRCA sequence from a text file, which has to be located in the same directory as the program.

All output files produced by the program are written to the folder Results.

The license of this software is Free, you can free download and free use this application software.