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Guide structure calculation: a critical step for the accuracy of progressive multiple sequence alignment algorithms

Abstract : Despite the importance of the guide structure calculation in progressive multiple sequence alignment algorithms, its influence on alignments accuracy was under studied. In this article, we test selected clustering and phylogenetic reconstruction methods, implemented in ClustalW, to compare their efficiency with the benchmark database Balibase. The evaluation of their performance gives statistically significant results. Three methods outperform the Neighbor-Joining, which is the algorithm implemented in ClustalW. Moreover, the best method appears to depend on tested reference set. These results provide guidelines for the improvement of progressive algorithms.
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Contributor : Evelyne Faivre <>
Submitted on : Tuesday, March 4, 2008 - 5:00:00 PM
Last modification on : Tuesday, June 30, 2020 - 4:04:07 PM

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  • HAL Id : hal-00260675, version 1

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Laure Vescovo, Jean-Christophe Aude, Géraldine Polaillon. Guide structure calculation: a critical step for the accuracy of progressive multiple sequence alignment algorithms. 4th European Conference of Computational Biology 2005 (ECCB 2005), Sep 2005, Madrid, Spain. pp.76. ⟨hal-00260675⟩

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