This command is used to format data or commands in the program. The correct usage is
begin <data or mrbayes>;
The two valid uses of the "begin" command, then, are
begin data;
begin mrbayes;
The "data" specifier is used to specify the beginning of a data block; your character data should follow. For example, the following is an example of a data block for four taxa and ten DNA sites:
begin data; dimensions ntax=4 nchar=10; format datatype=dna; matrix taxon_1 AACGATTCGT taxon_2 AAGGATTCCA taxon_3 AACGACTCCT taxon_4 AAGGATTCCT ; end;
The other commands -- dimensions, format, and matrix -- are discussed in the appropriate help menu. The only thing to note here is that the block begins with a "begin data" command. The "mrbayes" command is used to enter commands specific to the MrBayes program into the file. This allows you to automatically process commands on execution of the program. The following is a simple mrbayes block:
begin mrbayes; charset first = 1-10\3; charset second = 2-10\3; charset third = 3-10\3; end;
This mrbayes block sets off the three "charset" commands, used to predefine some blocks of characters. The mrbayes block can be very useful. For example, in this case, it would save you the time of typing the character sets each time you executed the file. Also, note that every "begin <data or mrbayes>" command ends with an "end". Finally, you can have so-called foreign blocks in the file. An example of a foreign block would be "begin paup". The program will simply skip this block. This is useful because it means that you can use the same file for MrBayes, PAUP* or MacClade (although it isn't clear why you would want to use those other programs).