The two methods of encrypting data are
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Substitution and transposition
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Block and stream
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Symmetric and asymmetric
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DES and AES
The two fundamental methods of encrypting data are based on how the encryption algorithm operates: block ciphers (which encrypt fixed-size blocks of data) and stream ciphers (which encrypt data as a continuous stream, bit by bit or byte by byte). Symmetric/asymmetric refers to key management, not the encryption method itself.
Symmetric encryption algorithms process data either a fixed-size chunk at a time (block ciphers, like AES operating on 128-bit blocks) or one bit/byte at a time as a continuous stream (stream ciphers, like RC4), making block and stream the two fundamental modes of operation for encrypting data. Symmetric vs. asymmetric describes key management (shared vs. public/private keys), a different axis of classification, and substitution/transposition describes classical, pre-computer cipher techniques.