[ Program Manual | User's Guide | Data Files | Databases ]
About the Wisconsin Package...
Interfaces to the Wisconsin Package
Using This Guide
Conventions Used in This Guide
How This Guide is Organized
Getting Help
Using Online Help
Navigating in Lynx
Using a Different Web Browser to Access Online Help
Using GCG Technical Support
Getting Wisconsin Package Training
Using Companion Documentation
Ordering Additional Documentation
Photocopying or Printing Documentation
The Wisconsin Package(TM) is an integrated package of over 130 programs that allows you to manipulate and analyze nucleic acid and protein sequences. Scientists from all over the world have collaborated to develop and refine the Wisconsin Package, making it a flexible tool with which to analyze your sequence data.
Among its many features, the Wisconsin Package gives you access to
The Wisconsin Package provides these interfaces for your analysis needs:
This User's Guide provides information about Wisconsin Package commands and concepts. It is designed to be both a beginner's guide to working with Wisconsin Package programs and an intermediate and advanced user's reference to general concepts that all the programs use as their foundation. This guide can serve as an introduction to the Package or as a tool to enhance existing skills.
You do not have to read this manual front-to-back. It is designed around common tasks that you will perform, with headings and subheadings that allow you to scan the pages easily and zoom in on the information you are interested in. Take some time to browse through these tasks. You may discover things that will make your work with the Package more efficient and effective.
Some conventions in this guide make the text easier to read. Becoming familiar with these conventions will help you efficiently extract the information in which you're interested.
A special typeface (Courier, also known as typewriter font) indicates characters you should type. For example, consider the following command line:
% mapsort [-INfile=]ggammacod.seq -BEGin=93 -END=315 -Default
Note: Do not type the square brackets [ ].
Replace the generic specification /directory/filename with the actual directory and filename, for example /project/gamma.map.
This guide is divided into five chapters, followed by appendices, a glossary, and an index. Use the following table as a general guide to find the information you need in the Wisconsin Package documentation.
| If you're interested in | Turn to |
| An overview of the operating system | Chapter 1, Getting Started |
| Starting the Wisconsin Package | Chapter 1, Getting Started |
| Specifics about using sequences | Chapter 2, Using Sequences |
| Databases | Chapter 2, Using Sequences |
| Learning about the basic concepts you will need to use the Wisconsin Package programs | Chapter 3, Using Programs |
| Learning how to run specific programs | Program Manual Command-Line Summary |
| Finding out about different data files, for example scoring matrices and restriction enzymes | Chapter 4, Using Data Files Appendix VII of the Program Manual |
| Learning more about Wisconsin Package programs that produce graphic output, how you can use and manipulate that output, and what graphics configuration languages are available | Chapter 5, Using Graphics Appendix C, Graphics |
| Printing ASCII or graphic files | Chapter 3, Using Programs Chapter 5, Using Graphics |
| A list of Wisconsin Package programs organized by function | Appendix A, Short Descriptions Functional table of contents list of the Program Manual Programs by Function chapter of the Command-Line Summary |
| Basic guidelines for using the text editor vi | Appendix B, Text Editor Basics |
| Differences between OpenVMS and UNIX | Appendix D, Command and Keystroke Differences Between OpenVMS and UNIX |
| Definitions of some terms found in this guide | Glossary |
If you find that you need additional help with the Wisconsin Package, check your paper documentation or online help. GCG also has a technical support staff which you can contact by telephone, fax, or e-mail. In addition, training services are available.
The online help for the Wisconsin Package is in HTML format and provides access to the Program Manual, User's Guide, User Release Notes, and data files.
You can choose between two types of help: GenHelp and GenManual. Both types include the same information, though organized differently.
The commands % genhelp and % genmanual automatically launch Lynx, a text-only web browser, which enables you to view the online help. (To use a web browser you are more familiar with, see "Using a Different Web Browser to Access Online Help" later in this section.) Following is the first screen for GenManual.
Note the summary of commands for using Lynx located at the bottom of the screen. For more information on navigating in Lynx, see the next section.
Note: To access online help for UNIX operating system commands, type % man command_name, for example % man ls.
To navigate in Lynx, use the following keys:
| To do this | Press |
| Highlight next link | <Down Arrow> |
| Highlight previous link | <Up Arrow> |
| Follow the link | <Return> or <Right Arrow> |
| Go back to previous document | <Left Arrow> |
| Go to top of document | <Ctrl>A |
| Go to end of document | <Ctrl>E |
| Page down | <Space Bar> |
| See a history list of previous links in your current session | <Delete> or <Backspace> |
Note: If your arrow keys don't work, press
o V <Space Bar> <Return> r
(That is, press lowercase letter "o", capital letter "V", <Space Bar>, <Return>, lowercase letter "r".)
This key combination will put Lynx into vi mode. You can then use the following keys for navigating:
h - Go back to previous document
j - Highlight next link
k - Highlight previous link
l - Follow the link
H - Get help
You may also find the following keys useful:
| To do this | Press |
| Get help | H, h or ? |
| Return to main GCG help page | m |
| p | |
| Quit Lynx | q |
| Search the current document | / |
| Reload document and refresh screen |
<Ctrl>R |
| Cancel a transfer in progress | z |
For a list of other helpful keystroke commands, see the topics "Lynx Users Guide" and "Key-stroke Commands" in Lynx's online help.
You can use a web browser you are more familiar with, such as Netscape or Internet Explorer, to access GCG's online help.
The first step is to get the URL (Universal Resource Locator) for GCG's online help at your site. To do so, type % gcgversions.
Your GCG manager should have inserted the URL for your site's online help in the GCG banner. (In this example, the URL appears toward the bottom of the screen).
After getting the URL for GCG's online help, choose between the following:
To save this definition and make it available each time you log in, add the command above to one of the following files: gcgrc (csh) or .gcgrc.ksh (ksh). For more information about command procedures, see "Working with Command Procedures" in Chapter 3, Using Programs.
GCG's technical support is available Monday through Friday from 8:30 a.m. to 5:30 p.m. Central Time. You can reach technical support staff by telephone, fax, or e-mail:
Phone: (608) 231-5200
Fax: (608) 231-5202
E-mail: help@gcg.com
When you call, you should be at your computer and be prepared to provide the following information, if possible:
Make sure you supply the GCG support person with your name, e-mail address/fax number/telephone number, and the name of your company or institution.
Genetics Computer Group offers training services tailored to your site.
Standard training courses include lecture and laboratory sessions. The lecture provides an overview of the Package, discussion of computer algorithms, and strategies for answering basic research questions. Laboratory sessions let you gain hands-on experience with the programs, learn how to interpret output files created, and ask questions specific to your research needs.
The training usually takes place at your site. However, small groups of users also have the option of training at GCG. The course varies between two and three days.
For more information about GCG's training services, call (608) 231-5200, fax (608) 231-5202, or e-mail training@gcg.com.
In addition to this command-line User's Guide, the Wisconsin Package documentation set includes the following manuals. Each site receives one copy of each of these manuals.
If your site has SeqLab, the graphical user interface to the Wisconsin Package, it also receives one copy of each of these manuals:
You can order additional copies of the documentation described above by calling (608) 231-5200, faxing (608) 231-5202, or e-mailing doc@gcg.com.
If you need help deciding which documentation best fits your needs, ask to speak to a technical support person before placing your order.
Genetics Computer Group permits photocopying of Wisconsin Package documentation for use by institutions that hold valid License Agreements. GCG also provides the Red documentation files for the Program Manual, which you can print without permission. (For more information on the Red program, see the Program Manual.) You can purchase binders and tabs from GCG to make locally produced documents more appealing.
[ Program Manual | User's Guide | Data Files | Databases ]
Documentation Comments: doc-comments@gcg.com
Technical Support: help@gcg.com
Copyright (c) 1982, 1983, 1985, 1986, 1987, 1989, 1991, 1994, 1995, 1996, 1997, 1998 Genetics Computer Group Inc., a wholly owned subsidiary of Oxford Molecular Group, Inc. All rights reserved.
Licenses and Trademarks Wisconsin Package is a trademark of Genetics Computer Group, Inc. GCG and the GCG logo are registered trademarks of Genetics Computer Group, Inc.
All other product names mentioned in this documentation may be trademarks, and if so, are trademarks or registered trademarks of their respective holders and are used in this documentation for identification purposes only.