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GCHQ CyberChef - The Cyber Swiss Army Knife - a web app for encryption, encoding, compression and data analysis. Web-based tool for general cypher processing, amongst many other features. Simple programming via drag-and-drop of components.
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Cryptool - Classical and modern cryptography implementations, intended as a learning platform to experiment with cryptography. Includes two Windows-only versions, a Java version, and an online tool. Includes descriptions of
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EverCrack - EverCrack performs cryptanalysis on mono-alphabetic substitution and transposition ciphers. Windows, Linux, and online versions.
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Ganzua - Ganzúa is a cryptanalysis tool for monoalphabetic and polyalphabetic ciphers that can work with almost any set of characters. Cross-platform (Java).
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CryptoCrack - Classical cipher solving program. Windows-only.
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quipquip - Web-based automatic substitution cipher cracker.
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ciphr - a CLI tool for performing and composing encoding, decoding, encryption, decryption, hashing, and other various cryptographic operations on streams of data from the command line.
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featherduster - Modular framework for cryptanalysis of modern cryptographic implementations.
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HashPump - A tool to exploit the hash length extension attack in various hashing algorithms.
CyberChef, Cryptool also do some modern crypto.