Comparative Analysis of Multiple Sequence Alignment Tools

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Eman M. Mohamed 1,* Hamdy M. Mousa 1 Arabi E. keshk 1

1. Faculty of Computers and Information, Menoufia University, Egypt

* Corresponding author.


Received: 24 Apr. 2018 / Revised: 11 Jun. 2018 / Accepted: 7 Jul. 2018 / Published: 8 Aug. 2018

Index Terms

Multiple Sequence Alignment, Accuracy, Progressive Alignment, Iterative alignment, and Bioinformatics


The perfect alignment between three or more sequences of Protein, RNA or DNA is a very difficult task in bioinformatics. There are many techniques for alignment multiple sequences. Many techniques maximize speed and do not concern with the accuracy of the resulting alignment. Likewise, many techniques maximize accuracy and do not concern with the speed. Reducing memory and execution time requirements and increasing the accuracy of multiple sequence alignment on large-scale datasets are the vital goal of any technique. The paper introduces the comparative analysis of the most well-known programs (CLUSTAL-OMEGA, MAFFT, BROBCONS, KALIGN, RETALIGN, and MUSCLE). For programs’ testing and evaluating, benchmark protein datasets are used. Both the execution time and alignment quality are two important metrics. The obtained results show that no single MSA tool can always achieve the best alignment for all datasets.

Cite This Paper

Eman M. Mohamed, Hamdy M. Mousa, Arabi E. keshk, "Comparative Analysis of Multiple Sequence Alignment Tools", International Journal of Information Technology and Computer Science(IJITCS), Vol.10, No.8, pp.24-30, 2018. DOI:10.5815/ijitcs.2018.08.04


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