This command allows you to specify a character partition. The format for this command is
partition <name> = <num parts>:<chars in first>, ...,<chars in last>
For example, "partition by_codon = 3:1st_pos,2nd_pos,3rd_pos" specifies a partition called "by_codon" which consists of three parts (first, second, and third codon positions). Here, we are assuming that the sites in each partition were defined using the charset command. You can specify a partition without using charset as follows:
partition by_codon = 3:1 4 6 9 12,2 5 7 10 13,3 6 8 11 14
However, we recommend that you use the charsets to define a set of characters and then use these predefined sets when defining the partition. Also, it makes more sense to define a partition as a line in the mrbayes block than to issue the command from the command line (then again, you may be a masochist, and want to do extra work).