Chapter

Sequence Evolution Models for Simultaneous Alignment and Phylogeny Reconstruction

Dirk Metzler and Roland Fleissner

in Sequence Alignment

Published by University of California Press

Published in print November 2009 | ISBN: 9780520256972
Published online March 2012 | e-ISBN: 9780520943742 | DOI: http://dx.doi.org/10.1525/california/9780520256972.003.0005
Sequence Evolution Models for Simultaneous Alignment and Phylogeny Reconstruction

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This chapter reviews the statistical approaches for simultaneous alignment and phylogeny reconstruction. It focuses on the modeling of insertion and deletion events in a phylogenetic framework, and on how recent advances in likelihood maximization and Bayesian methods enable these advanced statistical procedures to be used to align sequences. The chapter begins by discussing sequence evolution models used to model insertions and deletions (indels), and then describes the Markov-chain Monte Carlo methods for sampling multiple alignments and phylogenetic trees to their posterior distribution for given sequence data.

Keywords: simultaneous alignment; phylogeny reconstruction; likelihood maximization; Bayesian methods; sequence evolution models; indels; Monte Carlo methods; multiple alignments

Chapter.  8366 words.  Illustrated.

Subjects: Evolutionary Biology

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