Welcome to the EMBOSS Users Manual

Table of Contents

1. Chapter 1. Background to EMBOSS
2. Chapter 2. Basic Set-up and Maintenance
3. Chapter 3. Getting Started
4. Chapter 4. Tutorial
5. Chapter 5. File Formats
6. Chapter 6. The EMBOSS Command Line
7. Chapter 7. Interfaces
8. Chapter 8. Using EMBOSS under wEMBOSS
9. Chapter 9. Using EMBOSS under Jemboss
10. Appendix A. File Format Reference
11. Appendix B. Application Reference
12. Appendix C. Command-line Qualifier Reference
13. Appendix D. Resources

This manual was written with newcomers to EMBOSS in mind. You will benefit from at least a basic appreciation of molecular biology and some familiarity with UNIX. You should know how to open, use, save and close files using a text editor. It will also help if you've used the EMBOSS programs and are familiar with the command line.

All of the material in the EMBOSS Guides is available on the EMBOSS web site: