The article introduces the Genome Assembly Program (GAP), a new DNA sequence assembly program developed by James K. Bonfield, Kathryn F. Smith, and Rodger Staden. GAP is designed to handle both large and small sequencing projects, supporting a variety of strategies and data from different sequencing instruments. It builds upon previous work but introduces novel features and a highly interactive graphical user interface (GUI). The GUI provides visual cues to help users understand the state of their sequencing projects and allows intuitive interaction with data. GAP includes tools for displaying and manipulating data to solve and check difficult assemblies, especially in repetitive genomes. New displays in GAP include the Contig Selector, Contig Comparator, Template Display, Restriction Enzyme Map, and Stop Codon Map. These tools enable users to manage and analyze data more effectively. The program also allows multiple Contig Editors and Contig Joining Editors to run simultaneously on the same contig. A new 'Directed Assembly' algorithm and routines for detecting unfinished segments of sequence are also included, with suggestions for experimental solutions. The program's algorithms are written in ANSI C and FORTRAN 77, while the user interface is built using Tcl and Tk, providing a Motif style look and feel. GAP is used on X windows on various UNIX workstations, and its design allows users to control how data is viewed and processed. The program uses several alignment algorithms for its operations. The article describes the data sources, file formats, and data types used by GAP, as well as the algorithms and interactive features. It outlines the main functions of the program, including the ability to annotate and label readings and contigs using 'tags'. Tags are used for various purposes, including providing visual clues and controlling which parts of the sequence are processed. The program also includes functions for finding 'problems' and suggesting experimental solutions. GAP includes a new Directed Assembly algorithm that allows readings to be assembled into known positions, either based on Experiment Suggestion functions or using a directed sequencing strategy. The program also includes tools for creating sequence library ready files and improving its utility for handling diagnostic sequences. The authors conclude that GAP is a significant advancement in DNA sequence assembly software, offering improved efficiency and accuracy. The program is available for contact via email, and further information is available on the World Wide Web.The article introduces the Genome Assembly Program (GAP), a new DNA sequence assembly program developed by James K. Bonfield, Kathryn F. Smith, and Rodger Staden. GAP is designed to handle both large and small sequencing projects, supporting a variety of strategies and data from different sequencing instruments. It builds upon previous work but introduces novel features and a highly interactive graphical user interface (GUI). The GUI provides visual cues to help users understand the state of their sequencing projects and allows intuitive interaction with data. GAP includes tools for displaying and manipulating data to solve and check difficult assemblies, especially in repetitive genomes. New displays in GAP include the Contig Selector, Contig Comparator, Template Display, Restriction Enzyme Map, and Stop Codon Map. These tools enable users to manage and analyze data more effectively. The program also allows multiple Contig Editors and Contig Joining Editors to run simultaneously on the same contig. A new 'Directed Assembly' algorithm and routines for detecting unfinished segments of sequence are also included, with suggestions for experimental solutions. The program's algorithms are written in ANSI C and FORTRAN 77, while the user interface is built using Tcl and Tk, providing a Motif style look and feel. GAP is used on X windows on various UNIX workstations, and its design allows users to control how data is viewed and processed. The program uses several alignment algorithms for its operations. The article describes the data sources, file formats, and data types used by GAP, as well as the algorithms and interactive features. It outlines the main functions of the program, including the ability to annotate and label readings and contigs using 'tags'. Tags are used for various purposes, including providing visual clues and controlling which parts of the sequence are processed. The program also includes functions for finding 'problems' and suggesting experimental solutions. GAP includes a new Directed Assembly algorithm that allows readings to be assembled into known positions, either based on Experiment Suggestion functions or using a directed sequencing strategy. The program also includes tools for creating sequence library ready files and improving its utility for handling diagnostic sequences. The authors conclude that GAP is a significant advancement in DNA sequence assembly software, offering improved efficiency and accuracy. The program is available for contact via email, and further information is available on the World Wide Web.