Insertion-deletion models for dequence evolution and Bayesian sampling methods for multiple alignment
Seminar Room 1, Newton Institute
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. A precondition for this is the availability of biologically plausible sequence evolution models which are compatible with efficient alignment algorithms. We discuss a variant of the Thorne-Kishino-Felsenstein model, having equal rates of insertions and of deletions of sequence fragments, for more than two sequences related by a phylogenetic tree. Finally, we discuss the perspectives for statistical multiple alignment based on this type of model.
Most parts of this talk are based on joint work with Roland Fleissner, Arndt von Haeseler, Ana Arribas-Gil, and Anton Wakolbinger.
- http://www.informatik.uni-frankfurt.de/~metzler/MFWvH04.pdf - Article about insertion-deletion models and statistical alignment.
- http://www.math.uni-frankfurt.de/~stoch/software/mcmcsalut/index.html - Software for pairwise alignment sampling.
- http://bioinformatics.oxfordjournals.org/cgi/content/abstract/19/4/490 - Article about fragment insertion-deletion model.
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