Frequently Asked Questions

If you don't find the answer to your question here, please call us, or, if you prefer, describe your question in an email message to support@genecodes.com. Please include your full contact information and your registration number.

General

Questions of Current Interest

Licensing

Sequencher Server

Sequencher Keys

Maintenance and Support

Troubleshooting

Usage Tips

General

What are the current versions of Sequencher?

The current release of Sequencher and Forensic-enabled Sequencher for both Windows and Macintosh is version 4.9. If you are using an older version and would like to upgrade, please contact us.

What are the computer hardware requirements to run Sequencher?

The requirements for Sequencher are the same for PC and Macintosh computers, 150MB of free hard disk space and 512MB of memory.

What versions of the operating system does Sequencher support?

Sequencher version 4.7 is the last release that supported Windows NT and Macintosh OS X 10.2.8. Sequencher version 4.8 is the last release that supports Microsoft Windows 2000. Sequencher 4.9 is supported on Microsoft XP, Vista, and on Macintosh OS X version 10.3.9 and higher.

Does Sequencher work with the new Macintosh Intel processors?

Yes. The current Macintosh version of Sequencher works with Rosetta.

Can I open data from an automated sequencer in Sequencher?

One of the reasons that Sequencher is so popular is its display of data from automated sequencers. You can view both individual chromatogram files and aligned chromatogram files in Sequencher. If a file that you have from an automated sequencer does not open in Sequencher, please contact technical support.

How do I purchase Sequencher?

Sequencher is available directly from Gene Codes Corporation. You may use either a purchase order or a credit card. Please email us at gcinfo@genecodes.com, call us at 800.497.4939 (In the US) or +1.734.769.7249 (outside the US), or fax us at +1.734.769.7074 and we will refer you to the sales representative for your area. You can also purchase Sequencher from one of our international distributors.

Can I get a copy of Sequencher for evaluation before I buy?

Yes. A demo version of Sequencher is available for download free of charge. It has all the latest features and you can try it on your own sequence data. Saving, exporting, and printing are disabled in the demo version.

Are there any Sequencher training courses or tutorials?

Many of our users find Sequencher so intuitive that training rarely becomes a question. However, you can extract much more power from Sequencher if you become familiar with a broader range of features and functionality. If you have any questions about how to accomplish something in Sequencher, we encourage you to contact us at technical support. We also provide tools for more independent exploration of Sequencher.

The Sequencher Help includes a searchable version of the 4.9 user manual. The Help is context sensitive, so whenever you execute a Help command from within Sequencher, you will open an HTML page that addresses questions related to where you are in the program. Search tools navigate you through Help for information on specific topics, and the Appendix contains a glossary and other tools to make your use of Sequencher more powerful and efficient.

On this Web Site you will also find the Tour Guide, which walks you through much of Sequencher’s core functionality; such as converting auto-sequencing files to an assembled and edited contig. A printed version of the Tour Guide also accompanies the demo CD.

We also provide you with several PDF tutorials with sample data. Each tutorial focuses on a particular aspect of your workflow. You may want to start with the Trimming Sequence and Assembly Strategies tutorials and then move on to the Reference Sequence and Quality Scores tutorials. The Assemble by Name and Variance Table tutorials will introduce you to these powerful new functions. We also have a tutorial specific for mitochondrial analysis.

Sequencher training options include internet-based training, where you work closely with a Sequencher expert on your specific sequence analysis questions while you share a desktop. Finally, Gene Codes also offers on-site training, which can be adapted to suit the needs of your organization. Please contact gcinfo@genecodes.com for details on price and scheduling.

Are you the Sole Source provider of this software in the United States?

Yes, and we can provide you with a letter stating this on request.

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Questions of Current Interest

Does Sequencher import Vector NTI files?

Yes. Sequencher 4.9 imports MA4 files with all of their associated features.

Does Sequencher work with Windows Vista?

Sequencher 4.9 does work on Vista, the operating system recently introduced by Microsoft. If you currently have Sequencher 4.7 or under, please upgrade to 4.9 for complete Vista compatibility.

Does Sequencher work with 64 bit processors?

In general, the answer is yes. To find out if you need special drivers to support certain 64 bit processors on Windows, see the 64-bit System Compatibility tutorial.

Does the current Sequencher release work with Mac OS 10.5 (Leopard)?

Yes. Sequencher versions 4.8 and later work with OS 10.5 (Leopard)

Note: Versions 4.7 and earlier do not allow you to save projects in OS 10.5 and they must be upgraded to the current version.

Do Sequencher network tools function on OS 10.5?

The current version of the network tools do function on an OS 10.5 installation. You will require an update of the Sassafras Key Server software to version 6.1.2 or later and the latest version of the Sequencher network license key. Software updates are available here. An updated key is available from Gene Codes.

Does Sequencher work with Mac-Intel processors?

Yes. Sequencher versions 4.8 and later work with Rosetta.

Can I run Sequencher Server on Mac-Intel Processors?

Yes. Sequencher versions 4.8 and later are completely compatible with Intel-based OSX systems.

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Licensing

How is Sequencher licensed?

Sequencher is available in two product configurations; you can choose a standalone version for use on one computer at a time or you can choose the network-enabled version. Sequencher’s licensing plans accommodate all installations from single users to multi-site institutions.

If I buy a standalone license of Sequencher, on how many computers may I install Sequencher?

There is no limit to the number of computers on which you may install Sequencher. You may install Sequencher on your office computer or lab computer, share it with a colleague or take it home and use it on your laptop. All standalone versions of Sequencher come with a hardware key that enables the program to operate in full mode. When the key is attached, Sequencher is fully functional. When the key is not attached, you can still use Sequencher to open your projects and review your data.

If I buy a network license of Sequencher, on how many computers may I install Sequencher?

Gene Codes does not limit your number of installations, only the number of concurrent users, and all of your users will receive technical support.

Does a Sequencher license expire?

Sequencher licenses never expire so you can always use the version of Sequencher you originally purchased. In addition, you will receive upgrades to the latest version of Sequencher for as long as you are a member of the Maintenance Program.

Can I change from a standalone license to a network license (or vice-versa)?

Yes, you can always upgrade a standalone license to a network license or revert your network license to a standalone.

Can I change from a Mac license to a Windows license (or vice-versa)?

Although you have cross compatibility between Macintosh and Windows versions of Sequencher, these are two separate software programs so we can not offer an exchange between the two applications.

We do offer the option to have a stand-alone Sequencher key that will work when plugged into either a Mac or Windows computer. Contact your sales person for pricing by writing to gcinfo@genecodes.com or calling 734-769-7249. Platform independent licenses are not yet available for the network version as of this writing.

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Sequencher Server

What is Sequencher Server? What is KeyServer?

KeyServer is a license management application available from Sassafras Software. The network version of Sequencher includes a limited version of this software for managing Sequencher licenses on a network.

Sequencher licenses can be served over TCP/IP, AppleTalk, or IPX. Sequencher for Windows will work on a Novell Server network (although not on the Novell server itself), but the Macintosh version is not supported in this environment.

How do I choose a Sequencher Server?

The network requires that you designate one computer as your server. The server may be any Macintosh or Windows based computer in your network, but it is best if it has a static IP address and if it is left on at all times.

Do I need to be an IT specialist in order to install the Sequencher Server?

Unless your organization restricts you from installation privileges, you should be able to install your Sequencher Server. Using the instructions we provide, you can have your first client installation running in less than ten minutes. Of course, if you have any difficulties, please contact technical support.

How do I set up a Sequencher Server?

We provide detailed instructions, but here are the six basic steps to the installation process.

  1. Choose a computer to act as a server and identify its IP address.
  2. Install the Sequencher Server software on that computer.
  3. Identify the Client computers; those on which you want to run Sequencher.
  4. Install the client software, KeyAccess, on these computers.
  5. Use the KeyAccess setup program to log onto the server via TCP/IP.
  6. Install Sequencher on the client computers

If you have difficulty, please contact us at technical support so we can help you.

Can we add Sequencher licenses to an already existing KeyServer?

Yes, if you have the full version of KeyServer from Sassafras, it is possible to add Sequencher license management to it.

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Sequencher Keys

What is a Dongle? What is a Hardware Key?

Sequencher is supplied with a small device called a Dongle or Hardware Key which plugs into the back of your computer. Each time you use Sequencher the program checks for the presence of this device.

The Hardware Key is effectively the license to unlock Sequencher. Please protect it as you would any other valuable computer equipment; in case of loss or theft please contact your insurance company.

What types of Hardware Keys are available?

Both Windows and Macintosh versions of Sequencher and Sequencher Server come with a USB key. If you run Windows NT, which does not support USB, you can get a parallel port key.

What are the requirements for using a USB Key with Sequencher for Windows?

You must be using Windows 2000, XP, or Vista.

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Maintenance and Support

How do I get technical support for Sequencher?

Unlimited Sequencher technical support is available to all current members of the Maintenance Program by email and by phone. We encourage you to phone us, but if you prefer email, please complete the form on the Contact Support page, describing your problem as completely as possible. Include your full contact information and your registration number or the original purchaser's name. We also have a troubleshooting guide as part of this FAQ.

How do I find my registration number?

You will find your registration number on the front of a blue card included in the documentation shipped with Sequencher and also on the key. Your registration number may also be displayed on the splash screen when the program starts up, or in the window displayed when you select About Sequencher from the Help menu (the Sequencher menu on the Macintosh).

What is the Maintenance Program?

Gene Codes maintenance plan for Sequencher is an annual plan that provides you with valuable benefits such as unlimited technical support, and a guarantee of at least one upgrade. When you are covered under the maintenance plan there are no charges for overnight shipping of replacement CDs, technical consulting for sequencing projects, or rearrangement of your network configuration.

When you purchase Sequencher, you receive the first year's maintenance free of charge.

I never need technical support. Why should I enroll in the maintenance plan after the first year of coverage expires?

You should enroll because of the upgrades. In earlier years enrolling in the maintenance program, though valuable, was not as necessary as it is today. Now we, as users of technology, are faced with a constantly evolving environment. Many of the changes that we incorporate into new releases of Sequencher enable you to function on the latest operating systems, or to import new data file formats. When you continue to use older versions of Sequencher you lose the flexibility these updates provide.

How often do you release new versions of Sequencher?

We release at least one Macintosh and one Windows upgrade of Sequencher each year.

Can I swap my old ADB/ Parallel Port key for a USB?

Yes, if you are a current member of the Sequencher Maintenance Program. Just contact us, quoting your registration number.

I have old Sequencher licenses. Do I have to buy new licenses to get the latest version of Sequencher?

If you have allowed your maintenance program to lapse, it is possible to rejoin the plan with full benefits and receive the latest version of Sequencher. The cost of rejoining varies based on how long you have been off of maintenance, but it costs much less than purchasing a new license. Contact your sales representative for details.

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Troubleshooting

Why am I prompted for a password when I install Sequencher on my Macintosh?

The prompt is from your Macintosh operating system. When you install an application on OSX the operating system insures that you have administrative privileges by requiring a password.

When I start Sequencher, I see this message: Sequencher was unable to find a key. The program will run only in Demo Mode. What do I do?

This error message is possible for both standalone and network versions of Sequencher. Although the underlying causes differ greatly between the two license types, the error triggers because Sequencher is unable to obtain a license from either a hardware key attached to the machine running the program, or from a Sequencher Server or KeyServer network.

If you have a key attached to your computer…
Determine if your key is a standalone or network key. The number of users for network licenses is printed on the side of your key. If your key defines a number of users, then it is a network key.

If you are using a network key…
When you obtain a Sequencher license from a network key, you must log on to KeyServer using KeyAccess software, even if the network key is attached to your machine. A lost connection to the server is the most likely reason for triggering the demo mode error with a network license. To reconnect, confirm the IP address of your KeyServer, and then logon using KeyAccess. You can also use the KeyVerify utility, distributed on the server disk, and run it from your machine to check for problems obtaining a network license.

If you are using a standalone key…
There are four reasons that Sequencher will prompt you with this message if you are using a standalone key: 1) You have Sequencher 4.8 or earlier and you are using a Purple Eve 3 Macintosh standalone key; you must upgrade to the new SuperPro key (please contact Gene Codes sales department), 2) the key is broken, 3) the port is not configured correctly or compatible with your key (note Windows NT and earlier operating systems are not compatible with USB) 4) the installation did not include the driver for your key. To check if the key is broken, check to see that the light is on (USB only). If you have access to another standalone key, plug it in to see if that key enables your installation. Installing Sequencher on another machine is a good means of testing whether you have a configuration specific problem. If you don’t have the right drivers, try reinstalling Sequencher from your CD.

If you don’t have a key attached to your computer…
Then you must be using a network version of Sequencher. Follow the above recommendations for using a network key.

If none of the above solves your problem, please contact Sequencher support (support@genecodes.com), quoting your registration number.

I have updated my Windows operating system to Vista, and now Sequencher only launches in demo mode. What do I do?

The versions of Sequencher prior to 4.8 are not completely compatible with the Vista operating system. If you have Sequencher 4.7 or earlier and are running Windows Vista, please upgrade to a more current version.

I have upgraded my computer to OSX and my ADB key is no longer recognized. What do I do?

ADB ports are not supported by OSX. The recommended course of action is to exchange your ADB key for a USB key. Please contact us, quoting your registration number or the name of the original purchaser of Sequencher.

My Windows version of Sequencher doesn’t recognize the projects that I created on a Macintosh. What do I do?

Windows applications are more dependent on extensions than Macintosh applications. In order to open Sequencher projects that originate on a Macintosh add a *.SPF extension to the file.

I run my KeyServer on a Windows XP SP2 machine. I can run my client from the Server machine, but I am unable to log onto the server from other clients. What do I do?

The firewall in XP Service Pack II will not allow a remote client to log onto the server unless you open specific UDP ports. Below are two links which document how to get to the Windows Firewall administration panel and how to open ports. The two ports that need to be opened are UDP 19283 and UDP 19315.

http://www.microsoft.com/technet/community/columns/cableguy/cg0204.mspx

http://www.microsoft.com/windowsxp/using/security/internet/sp2_wfintro.mspx

Where can I find some example scripts to run Sequencher using AppleScript commands?

We have prepared some sample scripts to help you get started using AppleScript with Sequencher. Click here to download a zip file with several examples. If you develop scripts of your own that you'd like to share with the community, we'd be happy to pass them on. Contact us at support@genecodes.com

Some of my fonts do not look right on Japanese/Chinese/Korean versions of Windows XP and Vista. What should I do?

Some versions of Windows have problems with two-byte language systems and Microsoft provides a fix to that problem. Download a new ASIFONT.map file, then follow these simple steps:

  1. Make sure Sequencher is not running.
  2. Unzip the asifont.zip file.
  3. Go to your '<drive>\Program Files\Gene Codes\Sequencher 4.9' folder.
  4. Rename asifont.map that you find there as 'old asifont.map'.
  5. Copy the newly unzipped asifont.map file into that same folder.
  6. Relaunch Sequencher 4.9.

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Usage Tips

How do I import features from a GenBank sequence into Sequencher?

Sequencher imports all Genbank features with a defined range, including joined features, as editable features in Sequencher. To import any individual or concatenated sequence into Sequencher, use the IMPORT > SEQUENCE command.

How do I share Sequencher Macintosh and Sequencher Windows projects?

Project files created by version 4.1 and higher of Sequencher (Mac or Windows) are entirely cross-platform compatible. Additionally, Sequencher is backwards compatible with previous project file formats on the same platform (any Mac version of Sequencher can read project files created by a previous version of Sequencher on the Mac, and the same is true for Windows). It is therefore possible to read an old project file with a new version of Sequencher and then save it in the current cross-platform format.

Sequencher project files created on the Macintosh by version 3.1 of Sequencher are not cross-platform compatible. You can download a Mac-to-PC converter (Macintosh Classic version only).

How do I trim a sequence using vector parameters that are not included in VecBase?

Selecting Specify Vector Insertion Sites ... under the Window menu in Sequencher allows the user to define up to four pairs of flanking sequences to trim. These sequences may be loaded from a Vecbase file (one is supplied with Sequencher) or up to 250 bases of sequence may be manually entered for each pair of flanking sequences. You can optionally save your entries to a file for future use by selecting the Save Sites button.

How can I add vectors to Sequencher's VecBase file?

Here's how [PDF].(To read and print this document, you will need the free Adobe Acrobat Reader.)

How do I add restriction enzymes?

If you wish to use a restriction enzyme that is not in the default set of enzymes supplied with Sequencher, open a project and highlight the fragments or contigs for which you wish to specify the new enzyme. Select the Specify Restriction Enzymes ... option from the Window menu and check the Allow changes checkbox. You can then use the New Enzyme button to create a new enzyme record. Click the Done button when you are finished.

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