All molecular sequence data used by the PHASE programs are stored in a common format. The data file format is similar to the PHYLIP data file format but has a few minor modifications.
A data file is divided into four sections but two of them are not compulsory. Comments can be included by preceding the commented lines with a hash (#) symbol. The entire commented line is ignored by the program. Taking a look at the example data files in the package (*.dna, *.rna, and *.mix in the data directory) will make the following explanations easier to understand.