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The parameter file parfile contains a series of statements. MORGAN defines a statement set which is consistent for all the programs. Each program uses a subset of them; other statements are simply ignored and a warning message is issued. Many statements are optional with some default behavior.
Each statement must begin on a new line and begins with one of the MORGAN statement keywords. A statement consists of any number of lines. Case is not significant for the keywords. Only the first four letters of the keywords are significant. The order of the statements does not matter. If the same statement is repeated, the last one overrides previous ones and a warning is given in the output file. A # starts a comment so that the rest of the line is ignored. Either single or double quotation marks (' or ") can be used to delimit strings such as file names. Look at the warnings issued by MORGAN to make sure the parameters are as you intended.
The most common statements are for identifying input and output files (counterparts of the command line options) and for describing the input pedigree file format.
For a complete description of MORGAN statements, please see the documentation which comes with MORGAN in the files `README_userdoc' in the various program subdirectories.