The input is token based. A token is any string of non-whitespace surrounded by whitespace. Each time a token begins with a -, it is read to determine what follows it. The next token is then read and processed. The program will ignore any token that it doesn't recognize.
Case is important.
If there is some portion of the data file that you don't want read, just put in a '-skip' token. Everything will be ignored until an '-unskip' token. After the start token, there should be the token 'qtls' and a number to indicate the number of traits to be modelled. After this there should be a repeating sequence of a trait name, number of loci for that trait, then the chromosome, position, additive and dominance effects for each locus. Please give all traits unique names.