File content

The first non-comment section of the data file is a single line containing

1. the number of species
2. the length of the molecular sequences
3. a code which can be either DNA for usual unpaired molecular sequences or RNA for base-paired molecular sequences. In fact the purpose of this code is to indicate whether a pairing mask is present in the data file and you can use the code RNA even if some nucleotides are unpaired.

For example the line,
5 100 DNA
at the beginning of a data file indicates that there are five non-base-paired sequences of length 100 in the file.

For convenience a third code, MIXED, can be used instead of RNA when the user is using a concatenation of RNA loops and stems but should be avoided in other cases. More details on the specific meaning of the code MIXED are given in the class section. The lines,
10 300 RNA
and,
10 300 MIXED
both indicate that there are ten sequences of length 300 in the file and that a pairing mask is associated with them.