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Estimation of Reversible Substitution Matrices from Multiple Pairs of Sequences
KTH, Superseded Departments, Numerical Analysis and Computer Science, NADA.
Los Alamos National Laboratory.
1997 (English)In: Journal of Molecular Evolution, ISSN 0022-2844, E-ISSN 1432-1432, Vol. 45, no 6, 696-703 p.Article in journal (Refereed) Published
Abstract [en]

We present a method for estimating the most general reversible substitution matrix corresponding to a given collection of pairwise aligned DNA sequences. This matrix can then be used to calculate evolutionary distances between pairs of sequences in the collection. If only two sequences are considered, our method is equivalent to that of Lanave et al. (1984). The main novelty of our approach is in combining data from different sequence pairs. We describe a weighting method for pairs of taxa related by a known tree that results in uniform weights for all branches. Our method for estimating the rate matrix results in fast execution times, even on large data sets, and does not require knowledge of the phylogenetic relationships among sequences. In a test case on a primate pseudogene, the matrix we arrived at resembles one obtained using maximum likelihood, and the resulting distance measure is shown to have better linearity than is obtained in a less general model.

Place, publisher, year, edition, pages
1997. Vol. 45, no 6, 696-703 p.
Keyword [en]
Evolutionary distance, General reversible model, Rate matrix, Eigenvalues
National Category
Bioinformatics (Computational Biology)
URN: urn:nbn:se:kth:diva-39799DOI: 10.1007/PL00006274ISI: 000071307200014OAI: diva2:440459
QC 20110913Available from: 2011-09-13 Created: 2011-09-13 Last updated: 2011-09-13Bibliographically approved

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Arvestad, Lars
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