Evaluating the Accuracy and Efficiency of Multiple Sequence Alignment Methods
Open accessAbstract
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.
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By default, MAFFT chooses FFT-NS-2, the strategy optimized for speed, which is on par with the fastest MSA algorithms.
“By default, it chooses FFT-NS-2, the strategy optimized for speed, which is on par with the fastest MSA algorithms [29].”
From Study of the error correction capability of multiple sequence alignment algorithm (MAFFT) in DNA storage (2023) · cites this paper as [29]
MAFFT (FFT-NS-2) was used as a proof of concept because of its good accuracy and quasi-linear time for pairwise comparison.
“In this paper, we use a MSA software, MAFFT (FFT-NS-2), as a proof of concept on MSA’s error correction capability because of its good accuracy and quasi-linear time for pairwise comparison [29].”
From Study of the error correction capability of multiple sequence alignment algorithm (MAFFT) in DNA storage (2023) · cites this paper as [29]
MAFFT has good accuracy and takes only quasi-linear time for pairwise comparison.
“MAFFT has good accuracy and takes only quasi-linear time for pairwise comparison.”
From Study of the error correction capability of multiple sequence alignment algorithm (MAFFT) in DNA storage (2023) · cites this paper as [29]
MAFFT also provides strategies that are state-of-the-art in terms of alignment accuracy, such as L-INS-i, which is comparable to the most accurate algorithms.
“But it also provides strategies that are state-of-the-art in terms of alignment accuracy, such as L-INS-i [29], which is comparable to the most accurate algorithms.”
From Study of the error correction capability of multiple sequence alignment algorithm (MAFFT) in DNA storage (2023) · cites this paper as [29]
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- Authors
- Pervez, M. T., Babar, M. E., Nadeem, A., Aslam, M., Awan, A. R., Aslam, N., Hussain, T., Naveed, N., Qadri, S., Waheed, U., & Shoaib, M.
- Affiliations
- Virtual University of Pakistan (PK)
- University of Veterinary and Animal Sciences (PK)
- University of Engineering and Technology Lahore (PK)
- NFC Institute of Engineering and Technology (PK)
- University of Koblenz and Landau (DE)
- Islamia University of Bahawalpur (PK)
- Corresponding author
- Pervez, Muhammad Tariq
- ORCID
- Venue
- Evolutionary Bioinformatics
- Publisher
- SAGE Publications
- Published
- 2014-01
- Volume
- 10
- Pages
- 205-17
- ISSN
- 1176-9343 (ISSN-L)
- PMC
- PMC4267518
- OpenAlex
- W2044364290
- Cited by
- 48
- References
- 40
- Citations by year
- 2025: 5 · 2024: 6 · 2023: 4 · 2022: 7 · 2021: 6 · 2020: 7 · 2019: 3 · 2018: 3 · 2017: 2 · 2016: 3 · 2015: 2
- FWCI
- 0.96
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Evolutionary Bioinformatics (publishedVersion, cc-by-nc)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- University of Veterinary and Animal Sciences
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fractal and DNA sequence analysis
- Physical Sciences › Computer Science › Artificial Intelligence › Algorithms and Data Compression
- Keywords
- multiple sequence alignment, alignment accuracy, alignment speed, muscle, MAFFT, T-Coffee, sate, Clustal Omega, insertion rate, sequence length
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