This command includes characters that were previously excluded from the analysis. The correct usage is
include <number> <number> <number>
or
include <number> - <number>
or
include <charset>
or some combination thereof. Moreover, you can use the specifier "\" to include every nth character. For example, the following
include 1-100\3
would include every third character. As a specific example,
include 2 3 10-14 22
includes sites 2, 3, 10, 11, 12, 13, 14, and 22 from the analysis. Also,
include all
includes all of the characters in the analysis. Including all of the characters (even if many of them are bad) is a very total-evidence-like thing to do. Doing this will make a certain group of people very happy. On the other hand, simply using this program would make those same people unhappy.