Molecular Biology and Evolution, Vol 9, 1148-1162, Copyright © 1992 by Society for Molecular Biology and Evolution
JL Thorne and H Kishino
Widely used methods for phylogenetic inference, both those that require and
those that produce alignments, share certain weaknesses. These weaknesses
are discussed, and a method that lacks them is introduced. For each pair of
sequences in the data set, the method utilizes both insertion-deletion and
amino acid replacement information to estimate a pairwise evolutionary
distance. It is also possible to allow regional heterogeneity of
replacement rates. Because a likelihood framework is adopted, the standard
deviation of each pairwise distance can be estimated. The distance matrix
and standard error estimates are used to infer a phylogenetic tree. As an
example, this method is used on 10 widely diverged sequences of the second
largest RNA polymerase subunit. A pseudo-bootstrap technique is devised to
assess the validity of the inferred phylogenetic tree.
ORIGINAL ARTICLE
Freeing phylogenies from artifacts of alignment
Department of Genetics, University of Washington.
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