Abstract
Alignments between DNA or protein sequences are the best way of comparing sequences to determine if they are similar. The degree of similarity between different sequences, that is, the extent of conserved nucleotide or amino acid residues, can be used to make inferences about whether they share common ancestry, or have common structures and functions that may have arisen through convergent evolution. The subject of molecular phylogenetics or systematics is very complex and cannot be explored here. A good starting point is Of Urfs and Orfs by R. F. Doolittle (1). Other texts include Sequence Analysis in Molecular Biology Treasure Trove or Trivial Pursuit by G. von Heijne; Sequence Analysis Primer edited by M. Gribskov and J. Devereux; Fundamentals of Molecular Evolution by W.-H. Li and D. Graur; and several chapters in Computer Analysis of Sequence Data, Part II edited by A. M. and H. G. Griffin (2–4). The documentation that comes with programs such as Phylip and Paup are also instructive sources.
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References
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© 1997 Humana Press Inc.
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Clewley, J.P., Arnold, C. (1997). MEGALIGN. In: Swindell, S.R. (eds) Sequence Data Analysis Guidebook. Methods In Molecular Medicine™, vol 70. Springer, Totowa, NJ. https://doi.org/10.1385/0-89603-358-9:119
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DOI: https://doi.org/10.1385/0-89603-358-9:119
Publisher Name: Springer, Totowa, NJ
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