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

ABSTRACT:

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 gen

SUBMITTER: Boumajdi N 

PROVIDER: S-EPMC11600722 | biostudies-literature | 2024 Nov

REPOSITORIES: biostudies-literature