Journal Article

TreeWave: command line tool for alignment-free phylogeny reconstruction based on graphical representation of DNA sequences and genomic signal processing

Ibrahimi, Azeddine, Boumajdi, Nasma, Bendani, Houda, Belyamani, Lahcen

2024

Overview

Background Genomic sequence similarity comparison is a crucial research area in bioinformatics. Multiple Sequence Alignment (MSA) is the basic technique used to identify regions of similarity between sequences, although MSA tools are widely used and highly accurate, they are often limited by computational complexity, and inaccuracies when handling highly divergent sequences, which leads to the development of alignment-free (AF) algorithms. Results This paper presents TreeWave, a novel AF approach based on frequency chaos game representation and discrete wavelet transform of sequences for phylogeny inference. We validate our method on various genomic datasets such as complete virus genome sequences, bacteria genome sequences, human mitochondrial genome sequences, and rRNA gene sequences. Compared to classical methods, our tool demonstrates a significant reduction in running time, especially when analyzing large datasets. The resulting phylogenetic trees show that TreeWave has similar classification accuracy to the classical MSA methods based on the normalized Robinson-Foulds distances and Baker’s Gamma coefficients. Conclusions TreeWave is an open source and user-friendly command line tool for phylogeny reconstruction. It is a faster and more scalable tool that prioritizes computational efficiency while maintaining accuracy. TreeWave is freely available at https://github.com/nasmaB/TreeWave .

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Algorithms / Alignment / Alignment-free / Analysis / Anopheles / Approximation / Base Sequence / Bioinformatics / Biomedical and Life Sciences / Clustering / Computational Biology - methods / Computational Biology/Bioinformatics / Computer Appl. in Life Sciences / Computer applications / Computer graphics / Control / Datasets / Decomposition / Discrete Wavelet Transform / DNA embedding / DNA sequencing / Frequency chaos game representation / Gene sequencing / Genetic aspects / Genome comparison / Genome, Mitochondrial - genetics / Genomes / Genomic signal processing / Genomics / Genomics - methods / Graphical representations / Health aspects / Humans / Identification and classification / Life Sciences / Machine learning / Methods / Microarrays / Mitochondrial DNA / Nucleotide sequence / Nucleotide sequencing / Phylogenetics / Phylogeny / Reconstruction / Ribosomal DNA / rRNA / Sequence Alignment - methods / Sequence Analysis, DNA - methods / Signal processing / Similarity / Software / Wavelet Analysis / Wavelet transforms / Whole-genome phylogeny