PatchWorkPlot: simultaneous visualization of local alignments across multiple sequences.

Abstract

Revealing structural variations within and across populations is crucial for understanding their diversification mechanisms and roles. Existing tools for visualization of structural variations often require labor-intensive figure preparation and are limited in their ability to integrate annotations. We developed PatchWorkPlot, a tool for automated visualization of pairwise alignments of multiple annotated sequences as dot plots combined into a single matrix. PatchWorkPlot enables exploration of positions, breakpoints, and architectures of structural variations across two or more sequences. The tool supports customization of visualization parameters and produces high-resolution, publication-ready figures. PatchWorkPlot significantly reduces manual work and simplifies the generation of complex plots for various cases, from individual loci to large-scale comparative projects. PatchWorkPlot is implemented using Python 3 and is publicly available at GitHub: github.com/yana-safonova/PatchWorkPlot.