Stochastic Insertion-Deletion Processes and Statistical Sequence Alignment

Dirk Metzler (), Roland Fleißner (), Anton Wakolbinger () and Arndt von Haeseler ()
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Dirk Metzler: Goethe-Universität, FB Biologie und Informatik
Roland Fleißner: University of Idaho, Department of Mathematics
Anton Wakolbinger: Goethe-Universität, FB Mathematik
Arndt von Haeseler: Heinrich-Heine-Universität, Bioinformatik

A chapter in Interacting Stochastic Systems, 2005, pp 247-267 from Springer

Abstract: Summary The reconstruction of the history of a set of sequences is a central problem in molecular evolutionary biology. Typically this history is summarized in a phylogenetic tree. In current practice the estimation of a phylogenetic tree is a two-step procedure: first a multiple alignment is computed and subsequently a phylogenetic tree is reconstructed, based on the alignment. However, it is well known that the alignment and the tree reconstruction problem are intertwined. Thus, it is of great interest to estimate alignment and tree simultaneously. We present here a stochastic framework for this joint estimation. We discuss a variant of the Thorne-Kishino-Felsenstein model, having equal rates of insertions and of deletions of sequence fragments, for $$\ell $$ ≥ 2 sequences related by a phylogenetic tree. Finally, we review novel approaches to tree reconstruction based on insertion-deletion models.

Date: 2005
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Persistent link: https://EconPapers.repec.org/RePEc:spr:sprchp:978-3-540-27110-9_11

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DOI: 10.1007/3-540-27110-4_11

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