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A-liner: linear alignment visualizer for genome comparisons.

Miki Okuno·Takeshi Yamamoto·Yoshitoshi Ogura·Takehiko Itoh
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Abstract

SUMMARY: A-liner is a flexible command-line tool for linear visualization of genome-scale sequence alignments, supporting outputs from multiple aligners and integrated visualization of annotations, highlights, quantitative tracks, and coordinate scales. It is applicable to a wide range of organisms, from bacteria to large eukaryotic genomes, and facilitates efficient generation of publication-ready comparative genome visualizations. AVAILABILITY AND IMPLEMENTATION: The source code and example output files for a-liner are available in the GitHub repository: https://github.com/mokuno3430/a-liner. A-liner v1.1.0 has been archived on Zenodo at https://doi.org/10.5281/zenodo.19702001.

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SoftwareGenomicsSequence AlignmentGenomeJournal ArticleResearch Support, Non-U.S. Gov't

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Miki Okuno, Takeshi Yamamoto, Yoshitoshi Ogura, Takehiko Itoh. 2026-06-01. A-liner: linear alignment visualizer for genome comparisons.. https://doi.org/10.1093/bioinformatics%2Fbtag408

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