A key part to many ciphers and forms of encryption is a mixed alphabet at its base. This goes back to Julius Caesar and his system of encryption that was simple displacement. A caesar encryption of 1 results in:
original:abcdefghijklmnopqrstuvwxyz
encoded: BCDEFGHIJKLMNOPQRSTUVWXYZA
An enhancement upon this system is to add a particular keyword to the beginning of the sequence, and letting the rest of the alphabet 'slide' into place. The next example uses a keyword of 'fubar'
original:abcdefghijklmnopqrstuvwxyz
encoded: FUBARCDEGHIJKLMNOPQSTVWXYZ
This has the advantage of permutating the alphabet in as many different ways as there are words. Still, it has problems. After the initial key, the letters fall in alphabetically which can make it easier to break.

One method to alleviate this problem is to transpose the alphabet:

F U B A R
C D E G H
I J K L M
N O P Q S
T V W X Y
Z
Which then read column by column provides:
original:abcdefghijklmnopqrstuvwxyz
encoded: FCINTZUDJOVBEKPWAGLQXRHMSY

A variant on this for key words with repeating letters such as 'foo bar baz' where the repeated letters are left blank:

F O _ B A R _ _ Z
C D E G H I J K L
M N P Q S T U V W
X Y
Again, this is read column by column:
original:abcdefghijklmnopqrstuvwxyz
encoded: FCMXODNYEPBGQAHSRITJUKVZLW

Yet another variant is to not only leave the repeated letters blank, but also their places in the rest of the alphabet. Again the 'foo bar baz' key shall be used.

F O _ B A R _ _ Z
_ _ C D E _ G H I
J K L M N _ P Q _
S T U V W X Y _
Which, again read column by column provides:
original:abcdefghijklmnopqrstuvwxyz
encoded: FJSOKTCLUBDMVAENWRXGPYHQZI

Increasingly complex methods can be used - the most important thing is that both sides know the system used to create the mixed alphabet. This is not necessarly the entierty of the encryption process, but rather at the core of such polygraphic substitution ciphers as the four square cipher and the playfair cipher.

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