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A polyalphabetic cipher is any cipher based on substitution, using multiple substitution alphabets. The Vigenère cipher is probably the best-known example of a polyalphabetic cipher, though it is a simplified special case. The Enigma machine is more complex but still fundamentally a polyalphabetic substitution cipher.
The Alberti cipher by Leon Battista Alberti around 1467 was believed to be the first polyalphabetic cipher. Alberti used a mixed alphabet to encrypt a message, but whenever he wanted to, he would switch to a different alphabet, indicating that he had done so by including an uppercase letter or a number in the cryptogram. For this encipherment Alberti used a decoder device, his cipher disk, which implemented a polyalphabetic substitution with mixed alphabets.
Although Alberti is usually considered the father of polyalphabetic cipher, Prof. Ibrahim A. Al-Kadi's 1990 paper ( ref- 2) to the Swedish Royal Institute of Technology in Stockholm regarding the Arabic contributions to cryptology reported (based on a recently discovered ancient script) the knowledge of polyalphabetic ciphers 500 years before Alberti.
Dr. Al-Kadi reported on the Arabic scientist by the name of Abu Yusuf Yaqub ibn Is-haq Al-Kindi, who authored a book on cryptology the "Risalah fi Istikhraj al-Mu'amma" (Manuscript for the Deciphering Cryptographic Messages) circa 750 AD. Al-Kindi introduced cryptanalysis techniques (including those for polyalphabetic ciphers), classification of ciphers, Arabic Phonetics and Syntax and most importantly described the use of several statistical techniques for cryptoanalysis.
[This book apparently antedates other cryptology references by 300 years.] [It also predates writings on probability and statistics by Pascal and Fermat by nearly 800 years.]
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