ALIFRITZ: Simultaneous Statistical Multiple Alignment and Phylogeny Reconstruction
Introduction:
While the reconstruction of phylogenetic trees and the computation of multiple sequence alignments
are highly interdependent, these two areas of research lead quite separate lives. The former often making
use of stochastic modelling, which the latter normally does not. Despite the fact
that reasonable insertion and deletion models for sequence pairs were already introduced more than ten years ago,
they have only recently been applied to multiple alignment and only in their simplest version.
Our program implements a strategy based on simulated annealing which makes use of these models to infer
a phylogenetic tree for a set of DNA or protein sequences together with the sequences' indel history, i.e. their multiple
alignment augmented with information about the positioning of insertion and deletion events in the tree.
Reference:
The method is described in detail in the following article:
- Roland Fleißner, Dirk Metzler and Arndt von Haeseler,
Simultaneous Statistical Multiple Alignment and Phylogeny Reconstruction.
Syst. Biol., 54, 548-561. DOI: 10.1080/10635150590950371, PMID: 16085574
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