A cipher based on the use of a secret alphabet is not very secure; such ciphers are presented as puzzles in crossword puzzle magazines. To achieve security it is required to do something better.
Today, even to people not acquainted with cryptography, a number of possibilities suggest themselves. Originally, though, the new ideas came one at a time, separated by hundreds or thousands of years.
The basic ways to improve on simple substitution are the following:
Another way of improving on simple substitution is less obvious. Today, text is often converted from the letters, punctuation marks, digits, and other symbols you find on a typewriter to the binary bits of ASCII. Before that, other representations of text were used to substitute for the printed word, such as Morse code. The ancient Greeks used the Polybius square for signalling, by means of which each letter was represented by two groups of from one to five signal fires.
If a letter can be broken up into smaller pieces for purposes of signalling, those smaller pieces can also be used in a cipher. For example, one can take the letters of a message apart into smaller pieces, transpose the smaller pieces, and then put the pieces back together again into letters.
This is called fractionation, and is closely related to polygraphic substitution for two reasons; one is that both deal with different sized units - parts of letters and letters, or letters and pairs of letters - and the other is that fractionation is sometimes used as a method of polygraphic substitution.
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