From the command line type:
% ./phyloMOD.pl file1.fasta file2.fasta [file1.exon [file2.exon]]
% perl phyloMOD.pl file1.fasta file2.fasta [file1.exon [file2.exon]],
where file1 and file2 are in fasta format.
Exon files are optional and are like Vista/ Lagan annotation files: start and end of each gene, as well as the name, should be listed on one line. A greater than (>) or less than (<) sign should be placed before this line to indicate whether the gene is transcribed from the plus strand or minus strand, respectively. Numbering should always be according to the plus strand. Exons should then be listed individually with the word "exon", after the start and end of each exon. UTRs are annotated the same way as exons are, with the word "utr" replacing "exon". In the directory annotation you should find some examples.
At running time you will be prompted for a single parameter: the maximum distance which is allowed between two hits to include them in a single module. Since, by definition, a module is long a few hundred bp, the maximum distance between adjacent hits in a module should be between 50bp and 200bp. A suggested value is 100bp.