Reduced alphabets which lump together several amino-acids into one letter.

Reduced (redundant or simplified) alphabets are used to represent protein sequences using an alternative alphabet which lumps together several amino-acids into one letter, based on physico-chemical traits. For example, all the aliphatics (I,L,V) are usually quite interchangeable, so many sequence studies group them into one letter

Examples of reduced alphabets are available in:

http://viscose.ifg.uni-muenster.de/html/alphabets.html

The Murphy tables are from here:

Murphy L.R., Wallqvist A, Levy RM. (2000) Simplified amino acid alphabets for protein fold recognition and implications for folding. Protein Eng. 13(3):149-152

Bio.utils.reduce_sequence is used to take a Protein alphabet, and reduce it using one of the tables here, or a user-defined table.