Abstract
Multiple sequence alignment (MSA) is essential in phylogenetic, evolutionary and functional analysis. Several MSA tools are available in the literature. Here, we use several MSA tools such as ClustalX, Align-m, T-Coffee, SAGA, ProbCons, MAFFT, MUSCLE and DIALIGN to illustrate comparative phylogenetic trees analysis for two datasets. Results show that there is no single MSA tool that consistently outperforms the rest in producing reliable phylogenetic trees.
Highlights
Several multiple sequence alignment (MSA) methods are available in the literature
Results show that there is no single Multiple sequence alignment (MSA) tool that consistently outperforms the rest in producing reliable phylogenetic trees
We perform the evaluation of eight alignment methods, namely ClustalX 1.81 [4], Align-m 2.3 [5], T-Coffee 3.93 [6], SAGA 0.95 [7], ProbCons 1.08 [8], MAFFT 5.743 [9], MUSCLE 3.6 [10] and DIALIGN 2.2.1 [11] to test their ability to generate similar phylogenetic test trees with respect to reference
Summary
McClure and colleagues tested the ability of MSA methods to identify short motifs found in four datasets of homologous proteins [1]. Thompson and colleagues presented a systematic analysis and comparison of several alignment programs using the BaliBASE reference alignments as test cases [3]. Despite these comparison studies, choosing an alignment method which produces the nearest phylogenetic test tree (TT) to the reference tree (RT) is still open for discussion. We perform the evaluation of eight alignment methods, namely ClustalX 1.81 [4], Align-m 2.3 [5], T-Coffee 3.93 [6], SAGA 0.95 [7], ProbCons 1.08 [8], MAFFT 5.743 [9], MUSCLE 3.6 [10] and DIALIGN 2.2.1 [11] to test their ability to generate similar phylogenetic test trees with respect to reference
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