Galaxy is an interactive platform for large-scale genome analysis, combining existing genome annotation databases with a simple web portal to enable users to search remote resources, combine data from independent queries, and visualize results. The system's core is a flexible history system that stores user queries, performs operations like intersections, unions, and subtractions, and links to computational tools. Galaxy is accessible at http://g2.bx.psu.edu. Unlike traditional genome browsers, Galaxy allows users to gather and manipulate data from various sources in multiple ways. Every user action is recorded in the history system, enabling users to combine or refine queries, perform calculations, or extract and visualize sequences or alignments. Operations such as joining, union, intersection, and subtraction can be done via a simple interface. Galaxy differs from existing systems by its focus on genomic sequence and alignment analysis. It integrates genomic sequences, alignments, and functional annotations, allowing users to perform complex analyses without programming skills. For example, users can find SNPs within coding exons of the IGF-II gene by combining queries from the UCSC Table Browser and applying intersection operations. Galaxy also supports combining and comparing ENCODE data to identify promoters. It enables users to analyze data sets from various sources, such as empirical results and computational predictions, to determine properties associated with gene promoters. For instance, it can identify promoters that are highly conserved or show significant binding by TAF1. Galaxy provides tools for evolutionary analysis, including calculating synonymous (Ks) and non-synonymous (Ka) substitution rates using the Yang-Neilsen algorithm. This allows users to perform the Ka/Ks ratio test, a widely used predictor of selection acting on protein-coding regions. The sliding window Ka/Ks test provides more detailed insights into selection regimes. Galaxy is designed as a modular system with separate components for core functionality, user interface, and operation libraries. It supports various data formats, including BED, AXT, and MAF, and provides conversion tools for interoperability. The system is efficient, with quick response times for queries and a user-friendly history page that tracks query status. Galaxy maintains user histories and preferences, allowing personalized access. It supports multiple user identities and can be accessed via different web interfaces. The system is supported by funding from various institutions and is continually updated to enhance its functionality and usability.Galaxy is an interactive platform for large-scale genome analysis, combining existing genome annotation databases with a simple web portal to enable users to search remote resources, combine data from independent queries, and visualize results. The system's core is a flexible history system that stores user queries, performs operations like intersections, unions, and subtractions, and links to computational tools. Galaxy is accessible at http://g2.bx.psu.edu. Unlike traditional genome browsers, Galaxy allows users to gather and manipulate data from various sources in multiple ways. Every user action is recorded in the history system, enabling users to combine or refine queries, perform calculations, or extract and visualize sequences or alignments. Operations such as joining, union, intersection, and subtraction can be done via a simple interface. Galaxy differs from existing systems by its focus on genomic sequence and alignment analysis. It integrates genomic sequences, alignments, and functional annotations, allowing users to perform complex analyses without programming skills. For example, users can find SNPs within coding exons of the IGF-II gene by combining queries from the UCSC Table Browser and applying intersection operations. Galaxy also supports combining and comparing ENCODE data to identify promoters. It enables users to analyze data sets from various sources, such as empirical results and computational predictions, to determine properties associated with gene promoters. For instance, it can identify promoters that are highly conserved or show significant binding by TAF1. Galaxy provides tools for evolutionary analysis, including calculating synonymous (Ks) and non-synonymous (Ka) substitution rates using the Yang-Neilsen algorithm. This allows users to perform the Ka/Ks ratio test, a widely used predictor of selection acting on protein-coding regions. The sliding window Ka/Ks test provides more detailed insights into selection regimes. Galaxy is designed as a modular system with separate components for core functionality, user interface, and operation libraries. It supports various data formats, including BED, AXT, and MAF, and provides conversion tools for interoperability. The system is efficient, with quick response times for queries and a user-friendly history page that tracks query status. Galaxy maintains user histories and preferences, allowing personalized access. It supports multiple user identities and can be accessed via different web interfaces. The system is supported by funding from various institutions and is continually updated to enhance its functionality and usability.