NX4: a web-based visualization of large multiple sequence alignments

Abstract

Summary: Multiple Sequence Alignments (MSAs) are a fundamental operation in genome analysis. However, MSA visualizations such as sequence logos and matrix representations have changed little since the nineties and are not well suited for displaying large-scale alignments. We propose a novel, web-based MSA visualization tool called NX4, which can handle genome alignments comprising thousands of sequences. NX4 calculates the frequency of each nucleotide along the alignment and visually summarizes the results using a color-blind friendly palette that helps identifying regions of high genetic diversity. NX4 also provides the user with additional assistance in finding these regions with a ‘focus þ context’ mechanism that uses a line chart of the Shannon entropy across the alignment. The tool offers geneticists an easy-to-use and scalable analysis for large MSA studies. Availability and implementation: NX4 is freely available at https://www.nx4.io, and its source code at https://github.com/NX4/nx4. Contact: solanoroman.j@husky.neu.edu. Supplementary information: Supplementary data are available at Bioinformatics online