This command excludes characters from the analysis. The correct usage is
exclude <number> <number> <number>
or
exclude <number> - <number>
or
exclude <charset>
or some combination thereof. Moreover, you can use the specifier "\" to exclude every nth character. For example, the following
exclude 1-100\3
would exclude every third character. As a specific example,
exclude 2 3 10-14 22
excludes sites 2, 3, 10, 11, 12, 13, 14, and 22 from the analysis. Also,
exclude all
excludes all of the characters from the analysis. Excluding all characters does not leave you much information for inferring phylogeny.