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.
Extra whitespace is ignored, so you can put in spaces, tabs, carriage returns, etc, to format your data in an understandable fashion. 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. Inbred Ri1 Recombinant inbred lines Sib Recomb. Test crosses -traits 2 give an integer value for the number of quantitative traits, that is those that have some numerical value for the phenotype.