title: Freeing phylogenies from artifacts of alignment.
abstract: 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.
authors.affiliation: Department of Genetics, University of Washington.
authors.forename: J L
authors.initials: JL
authors.lastname: Thorne
authors.forename: H
authors.initials: H
authors.lastname: Kishino
mesh_terms: D001483:Base Sequence; D017343:Genes, Plant; D016013:Likelihood Functions; D008969:Molecular Sequence Data; D010802:Phylogeny; D012273:Ribulose-Bisphosphate Carboxylase / Q000235:genetics; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D012273:Ribulose-Bisphosphate Carboxylase