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TreeWave: command line tool for alignment-free phylogeny reconstruction based on graphical representation of DNA
Nasma Boumajdi1, Houda Bendani1, Lahcen Belyamani2,3,4
1Laboratory of Biotechnology (MedBiotech), Rabat Medical & Pharmacy School, Bioinova Research Center, Mohammed V University in Rabat, Rabat, Morocco.
BMC Bioinformatics
|November 28, 2024
Summary
TreeWave is a new alignment-free algorithm for faster and more accurate phylogenetic tree reconstruction. This bioinformatics tool significantly reduces computation time for large genomic datasets while maintaining high accuracy.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Genomic sequence similarity comparison is vital in bioinformatics.
- Multiple Sequence Alignment (MSA) is standard but computationally complex and inaccurate for divergent sequences.
- Alignment-free (AF) algorithms offer an alternative to MSA.
Purpose of the Study:
- Introduce TreeWave, a novel alignment-free (AF) approach for phylogeny inference.
- Utilize frequency chaos game representation and discrete wavelet transform for sequence analysis.
- Provide a user-friendly, open-source command-line tool for rapid phylogenetic reconstruction.
Main Methods:
- Developed TreeWave using frequency chaos game representation and discrete wavelet transform.
- Applied TreeWave to diverse genomic datasets: viral, bacterial, human mitochondrial, and rRNA sequences.
- Validated TreeWave's performance against classical MSA methods.
Main Results:
- TreeWave demonstrated a significant reduction in running time, particularly for large genomic datasets.
- Phylogenetic trees generated by TreeWave showed comparable classification accuracy to MSA methods.
- Performance was assessed using normalized Robinson-Foulds distances and Baker's Gamma coefficients.
Conclusions:
- TreeWave is an efficient, scalable, and accurate open-source tool for phylogeny reconstruction.
- The algorithm prioritizes computational efficiency without compromising accuracy.
- TreeWave is freely available for research use.
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