title: Evaluating the accuracy and efficiency of multiple sequence alignment methods.
abstract: A comparison of 10 most popular Multiple Sequence Alignment (MSA) tools, namely, MUSCLE, MAFFT(L-INS-i), MAFFT (FFT-NS-2), T-Coffee, ProbCons, SATe, Clustal Omega, Kalign, Multalin, and Dialign-TX is presented. We also focused on the significance of some implementations embedded in algorithm of each tool. Based on 10 simulated trees of different number of taxa generated by R, 400 known alignments and sequence files were constructed using indel-Seq-Gen. A total of 4000 test alignments were generated to study the effect of sequence length, indel size, deletion rate, and insertion rate. Results showed that alignment quality was highly dependent on the number of deletions and insertions in the sequences and that the sequence length and indel size had a weaker effect. Overall, ProbCons was consistently on the top of list of the evaluated MSA tools. SATe, being little less accurate, was 529.10% faster than ProbCons and 236.72% faster than MAFFT(L-INS-i). Among other tools, Kalign and MUSCLE achieved the highest sum of pairs. We also considered BALiBASE benchmark datasets and the results relative to BAliBASE- and indel-Seq-Gen-generated alignments were consistent in the most cases.
authors.affiliation: Department of Computer Science, Virtual University of Pakistan, Lahore, Pakistan. ; Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan.
authors.forename: Muhammad Tariq
authors.initials: MT
authors.lastname: Pervez
authors.affiliation: Department of Bioinformatics, Virtual University of Pakistan, Lahore, Pakistan.
authors.forename: Masroor Ellahi
authors.initials: ME
authors.lastname: Babar
authors.affiliation: Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan.
authors.forename: Asif
authors.initials: A
authors.lastname: Nadeem
authors.affiliation: Department of Computer Science and Engineering, University of Engineering and Technology, Lahore, Pakistan.
authors.forename: Muhammad
authors.initials: M
authors.lastname: Aslam
authors.affiliation: Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan.
authors.forename: Ali Raza
authors.initials: AR
authors.lastname: Awan
authors.affiliation: Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan. ; Department of Computer Science, NFC Institute of Engineering and Technological Training, Multan, Pakistan.
authors.forename: Naeem
authors.initials: N
authors.lastname: Aslam
authors.affiliation: Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan.
authors.forename: Tanveer
authors.initials: T
authors.lastname: Hussain
authors.affiliation: University of Koblenz-Landau, Germany.
authors.forename: Nasir
authors.initials: N
authors.lastname: Naveed
authors.affiliation: Department of Computer Science, Islamia University of Bahawalpur, Pakistan.
authors.forename: Salman
authors.initials: S
authors.lastname: Qadri
authors.affiliation: Department of Computer Science, Virtual University of Pakistan, Lahore, Pakistan.
authors.forename: Usman
authors.initials: U
authors.lastname: Waheed
authors.affiliation: Department of Computer Science and Engineering, University of Engineering and Technology, Lahore, Pakistan.
authors.forename: Muhammad
authors.initials: M
authors.lastname: Shoaib
keywords: Multiple Sequence Alignment Tools; column score; comparative study of MSA tools; evolutionary parameters; sum of pairs score