title: Assessing variability by joint sampling of alignments and mutation rates.
abstract: When two sequences are aligned with a single set of alignment parameters, or when mutation parameters are estimated on the basis of a single "optimal" sequence alignment, the variability of both the alignment and the estimated parameters can be seriously underestimated. To obtain a more realistic impression of the actual uncertainty, we propose sampling sequence alignments and mutation parameters simultaneously from their joint posterior distribution given the two original sequences. We illustrate our method with human and orangutan sequences from the hyper variable region I and with gene-pseudogene pairs.
authors.affiliation: Johann Wolfgang Goethe-Universität, Fachbereich Mathematik, D-60054 Frankfurt am Main, Germany. dmetzler@math.uni-frankfurt.de
authors.forename: D
authors.initials: D
authors.lastname: Metzler
authors.forename: R
authors.initials: R
authors.lastname: Fleissner
authors.forename: A
authors.initials: A
authors.lastname: Wakolbinger
authors.forename: A
authors.initials: A
authors.lastname: von Haeseler
mesh_terms: D000818:Animals; D019143:Evolution, Molecular; D006801:Humans; D016013:Likelihood Functions; D015233:Models, Statistical; D011148:Pongo pygmaeus; D011544:Pseudogenes; D016415:Sequence Alignment / Q000379:methods*