Improving progressive alignment for phylogeny reconstruction using parsimonious guide-trees

Document Type

Conference Proceeding

Publication Date

12-1-2006

Abstract

Phytogenies are widely used for understanding the evolutionary histories of species and gene products. Maximum parsimony (MP) and maximum likelihood (ML) are commonly used optimization criteria for constructing phylogenies. However, phylogenetic descriptions depend not only on the employed reconstruction technique, but also on the underlying sequence alignment. Here, we establish a simple prescription to improve the underlying alignments used in phytogeny reconstruction. We adapt Gotoh's iterative strategy for improving a progressive alignment (by using better guide-trees) specifically for the purpose of constructing optimal MP phylogenies. We improve the progressive alignment heuristic as implemented in the MUSCLE alignment program by iterating with maximum parsimony guide-trees constructed using PAUP*, yielding both deterministic and randomized heuristics. We evaluate accuracy on simulated data under a wide range of model conditions and show that phylogenies produced using our technique are more accurate than phylogenies on other alignments. © 2006 IEEE.

Identifier

34547402408 (Scopus)

ISBN

[0769527272, 9780769527277]

Publication Title

Proceedings Sixth IEEE Symposium on Bioinformatics and Bioengineering Bibe 2006

External Full Text Location

https://doi.org/10.1109/BIBE.2006.253329

First Page

159

Last Page

164

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