%0 Journal Article
	%A Khaddouja Boujenfa and  Nadia Essoussi and  Mohamed Limam
	%D 2008
	%J International Journal of Computer and Information Engineering
	%B World Academy of Science, Engineering and Technology
	%I Open Science Index 20, 2008
	%T Comparison of Phylogenetic Trees of Multiple Protein Sequence Alignment Methods
	%U https://publications.waset.org/pdf/4182
	%V 20
	%X Multiple sequence alignment is a fundamental part in
many bioinformatics applications such as phylogenetic analysis.
Many alignment methods have been proposed. Each method gives a
different result for the same data set, and consequently generates a
different phylogenetic tree. Hence, the chosen alignment method
affects the resulting tree. However in the literature, there is no
evaluation of multiple alignment methods based on the comparison of
their phylogenetic trees. This work evaluates the following eight
aligners: ClustalX, T-Coffee, SAGA, MUSCLE, MAFFT, DIALIGN,
ProbCons and Align-m, based on their phylogenetic trees (test trees)
produced on a given data set. The Neighbor-Joining method is used
to estimate trees. Three criteria, namely, the dNNI, the dRF and the
Id_Tree are established to test the ability of different alignment
methods to produce closer test tree compared to the reference one
(true tree). Results show that the method which produces the most
accurate alignment gives the nearest test tree to the reference tree.
MUSCLE outperforms all aligners with respect to the three criteria
and for all datasets, performing particularly better when sequence
identities are within 10-20%. It is followed by T-Coffee at lower
sequence identity (30%), trees scores of all methods
become similar.
	%P 2845 - 2850