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Multiple Sequence Alignment in Phylogenetic Analysis (2000)
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BibTeX
@MISC{Phillips00multiplesequence,
author = {Aloysius Phillips and Daniel Janies and Ward Wheeler},
title = { Multiple Sequence Alignment in Phylogenetic Analysis},
year = {2000}
}
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Abstract
Multiple sequence alignment is discussed in light of homology assessments in phylogenetic research. Pairwise and multiple alignment methods are reviewed as exact and heuristic procedures. Since the object of alignment is to create the most efficient statement of initial homology, methods that minimize nonhomology are to be favored. Therefore, among all possible alignments, the one that satisfies the phylogenetic optimality criterion the best should be considered the best alignment. Since all homology statements are subject to testing and explanation this way, consistency of optimality criteria is desirable. This consistency is based on the treatment of alignment gaps as character information and the consistent use of a cost function (e.g., insertion–deletion, transversion, and
Keyphrases
multiple sequence alignment phylogenetic analysis insertion deletion phylogenetic research homology assessment initial homology character information optimality criterion phylogenetic optimality criterion possible alignment homology statement alignment gap cost function minimize nonhomology consistent use heuristic procedure efficient statement multiple alignment method
