There are eight perl scripts in total, four files for simulating overlapping genes and calculating the corresponding selection strengths, and the other four files for calculating selection strenghs for genes of interest.

The names of the files tell the phase and function of the scripts, for example, sas11_simulation.pl will simulate sense-antisense overlapping where the first codon position in the ORF1 (sense strand) overlaps with the first codon position in ORF2 (antisense strand). And sas11_data.pl will calculate the selection strength for a pre-known sas11 overlapping gene. 

The xxxxx_data.pl scripts will only take overlapping coding region of the overlapping genes as input, otherwise if there is a stop codon in the middle, the program will report an error. One must make sure that the overlapping phase of the interested gene matches the phase of script.

There's only one file for sense-sense overlap. Users need to make sure that the first codon position of ORF1 starts from the first base of input sequence, and the first codon position of ORF2 starts from the second base of the input sequence. 



For XXXX_data.pl, users need to input transition transversion ratio R and the sequence of dna1 and dna2 at the begining of the script. Example sequences are provided.



For XXXX_simulation.pl, users need to input size_of_set, which is the total number of sequences pairs to be simulated, number_of_codons, which is the expected length of the first ORF, distance, which is the proportion of changes per neutral site, dnds_1 is the selection strength for ORF1, and dnds_2 is the selection strength for ORF2, and R is transition transversion ratio.