2. Common Features and File Formats

All MORGAN programs use the same command line syntax, share many statements, and use the same pedigree data format. Most of the MORGAN programs need at least two input files in order to run: one parameter file and one pedigree data file. The parameter file contains computing requests, model parameters and input/output file options. It may also contain genotype data or other information specific to a particular MORGAN program. The pedigree file contains, at minimum, information on family relationships among the individuals in the sample. If the general syntax and format descriptions of this section seem complex, readers may find it easier to proceed to the actual examples of the following chapter. In the context of those examples, the general format may become clearer.

It is worth pointing out that white space in any input file is defined to be any of these characters: `,' (comma), `\t' (horizontal tab), `\v' (vertical tab), `\n' (line feed, or newline), `\f' (form-feed), `\r' (carriage return).

2.1 Command syntax
2.2 Parameter file
2.3 File identification statements
2.4 Pedigree file
2.5 Pedigree file description statements