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Substitution Matrices

  1. Stephen F Altschul

Published Online: 14 MAR 2008

DOI: 10.1002/9780470015902.a0005265.pub2



How to Cite

Altschul, S. F. 2008. Substitution Matrices. eLS. .

Author Information

  1. National Center for Biotechnology Information, Bethesda, Maryland, USA

Publication History

  1. Published Online: 14 MAR 2008

This is not the most recent version of the article. View current version (15 APR 2013)


A substitution matrix is a collection of scores for aligning nucleotides or amino acids with one another. These scores generally represent the relative ease with which one nucleotide or amino acid may mutate into or substitute for another, and they are used to measure similarity in sequence alignments.


  • alignment score;
  • sequence similarity;
  • gap costs;
  • PAM matrices;
  • BLOSUM matrices