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A-liner: linear alignment visualizer for genome comparisons
Miki Okuno1, Takeshi Yamamoto1, Yoshitoshi Ogura1
1Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Kurume, Fukuoka 830-0011, Japan.
Bioinformatics (Oxford, England)
|June 25, 2026
Summary
A-liner is a command-line tool that generates linear visualizations for genome-scale sequence alignments. This flexible tool supports multiple aligner outputs and integrates annotations for publication-ready comparative genomics.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Genome visualization is crucial for comparative genomics.
- Existing tools may lack flexibility in handling diverse aligner outputs and integrated data types.
Purpose of the Study:
- To introduce A-liner, a novel command-line tool for linear genome-scale sequence alignment visualization.
- To provide a flexible and integrated solution for comparative genome visualization across various organisms.
Main Methods:
- A-liner is a command-line tool developed for generating linear visualizations.
- It supports input from multiple sequence alignment tools.
- The tool integrates visualization of annotations, highlights, quantitative tracks, and coordinate scales.
Main Results:
- A-liner generates publication-ready comparative genome visualizations.
- The tool is applicable to a wide range of organisms, from bacteria to large eukaryotic genomes.
- It facilitates efficient visualization of complex genomic data.
Conclusions:
- A-liner is a versatile command-line tool for linear visualization of genome-scale sequence alignments.
- It effectively integrates diverse data types and supports multiple aligner outputs.
- The tool enhances the generation of publication-ready comparative genome visualizations for various organisms.
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