The current release of Sequencher for Windows is version 5.0 and Sequencher for Mac is 5.0.1. If you are currently using an older version and would like to upgrade, please contact us.
FAQ
These are some of our more Frequently Asked Questions (FAQs). If there's a question that you have that isn't answered on this page, please contact Technical Support or email to support@genecodes.com.
General
What is the current version of Sequencher?
How often do you release new versions of Sequencher?
We release at least one new Windows and Mac upgrade of Sequencher each year.
Does Sequencher work with 64 bit processors?
In general, the answer is yes. Sequencher 4.10.1 will automatically install 64 bit drivers on 64 bit operating systems. Versions of Sequencher prior to 4.10.1 will not install any drivers on 64 bit operating systems. Please download and install the 64 bit compatible drivers.
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 can contact us in the following ways:
- Call us at 1.800.497.4939 (in the US), or +1.734.769.7249 (outside the US)
- Email us at gcinfo@genecodes.com, or
- Fax us at +1.734.769.7074 and we will refer you to the sales representative for your area.
You may use either a purchase order or a credit card.
You can also purchase Sequencher from one of our International Distributors as well.
Can I get a copy of Sequencher for evaluation before I buy?
Yes. A demo version of Sequencher is available. Just fill out the Demo Download Form and you'll be given a confirmation page to download the demo free of charge.
It has all the latest features and you can try it with your own sequence data. However, copying data into other applications, saving, exporting, viewing reports, and printing are all 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 more familiar with a broader range of features and functionality that it can offer. 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 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.
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 tutorial will introduce you to these powerful 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.
Hardware - Windows Users
What are the computer hardware requirements to run Sequencher on Windows?
The minimal requirements to run Sequencher on Windows is 150MB of free hard disk space and 512MB of memory.
Does Sequencher work with Windows 7 & Vista?
Sequencher 5.0 does work with Windows 7 & Vista. If you currently have Sequencher 4.7 or under, please upgrade to 5.0 for complete Windows compatibility.
What versions of the Windows Operating System does Sequencher support?
Sequencher 4.8 and higher are supported on Windows 7, Vista, and XP.
Sequencher 4.8 is also the last release that supports Windows 2000. Sequencher 4.7 is the last release that supported Windows NT. Sequencher 4.7 is not supported on Microsoft Vista or Windows 7 without an install of the Sentinel SuperPro drivers. You can go to SafeNet’s website for the latest driver download.
Hardware - Mac Users
What are the computer hardware requirements to run Sequencher on Mac?
The minimal requirements to run Sequencher on Mac is 175MB of free hard disk space and 512MB of memory.
Does the current Sequencher release work with Mac OS 10.6 (Snow Leopard)?
Yes. Sequencher versions 4.8 and later work with Mac OS 10.6 (Snow Leopard).
Does the current Sequencher release work with Mac OS 10.7 (Lion)?
Yes, starting with Sequencher version 5.0.1.
What versions of Mac does Sequencher support?
Sequencher 4.7 was the last release that supported Mac OSX 10.2.8.
Sequencher 4.10.1 was the last release to support Mac OSX 10.3 & 10.4.
Sequencher 5.0 requires Mac OSX 10.5 or 10.6.
Sequencher 5.0.1 requires Mac Intel OSX 10.5, 10.6, or 10.7.
Since Sequencher 5.0.1 is now a native Intel Mac application, it will not run on PowerPC's. You can install but it will not run.
Does Sequencher work with Mac Intel Processors?
Yes. The 5.0 Mac version of Sequencher works with Rosetta. Sequencher 5.0.1 runs natively on Mac, so it does not require Rosetta and also runs on Mac OS 10.7 (Lion).
Can I run Sequencher Server on Mac-Intel Processors?
Yes. Sequencher versions 4.8 and later are completely compatible with Intel-based OSX systems.
Do Sequencher network tools function on Mac OS 10.7 (Lion)?
The current version of the network tools is functional on OS 10.5, 10.6, and 10.7. 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 on our Sequencher Server Download page. An updated key is available from Gene Codes.
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, how many computers can I install it on?
There is no limit to the number of computers on which you may install Sequencher. You may install Sequencher on your office computer, lab computer, share it with a colleague, or even 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.
What about Network Licensing? How many computers can I install it on?
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 at anytime.
Can I change from a Windows license to a Mac license (or vice-versa)?
Although you have cross compatibility between Windows and Mac 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.
Sequencher Server
What is Sequencher License 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 should I choose a Sequencher License 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 or DNS name and is left on at all times.
Do I need to be an IT specialist in order to install Sequencher Server?
Unless your organization restricts you from installation privileges, you should be able to install your Sequencher License Server on your own. 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 License Server?
We provide detailed instructions, but here are the six basic steps to the installation process.
- Choose a computer on your network to act as a Sequencher License Server.
- Run the Sequencher License Installer on that computer to install KeyServer and all the files necessary to recognize Sequencher licenses.
- Plug in the USB hardware key as the installer directs (it contains your licenses.
- At the end of the installation process, the IP address of the Sequencher License Server computer will be displayed. Write it down. You'll need that address to set up each client computer to run Sequencher.
- Install the client software, KeyAccess, on each of these computers by running the Sequencher Client/Setup.exe on Windows, or K2Client on OS X. You'll be asked to type in the address of the Sequencher License Server computer.
- Run the Sequencher Installer and Restart.
If you have any difficulty with the installation process, please Contact Technical Support.
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.
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 7, Vista, XP, or 2000. Any older Windows OS will not be able to use a USB key.
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 Request Tech 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 that could answer any of your questions as well.
How do I find my Registration Number?
You will find your registration number on the key that was shipped with your copy of Sequencher. 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 Mac).
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 with the world as it is today, we 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.
Can I swap my old ADB/Parallel Port Key for a USB Key?
Yes, if you are a current member of the Sequencher Maintenance Program. Just contact us by phone or email, and have your registration number on hand.
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.
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.
I have updated my Windows Operating System to Windows 7 or 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 Windows 7 or Vista. If you have Sequencher 4.7 or earlier and are running Windows 7 or Vista, please either upgrade to a more current version or install the latest sentinel drivers from SafeNet.
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 Licenses. 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 License 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 login using KeyAccess.
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 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 Technical Support, or email support@genecodes.com, quoting your registration number.
I have upgraded my Mac 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 my Mac version. What do I do?
Windows applications are more dependent on extensions than Mac applications. In order to open Sequencher projects that originate on a Mac, add a .SPF extension to the file if one does not already exist.
I run my KeyServer on a Windows 7, Vista, or 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 Windows 7, Vista, and XP Service Pack 2 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
Some of my fonts do not look right on Japanese/Chinese/Korean versions of Windows 7, Vista, or XP. What should I do?
Some versions of Windows have problems with two-byte language systems and Microsoft has provided a fix to that problem. Download a new ASIFONT.map file, then follow these simple steps:
- Make sure Sequencher is not running.
- Unzip the asifont.zip file.
- Go to your '<drive>\Program Files\Gene Codes\Sequencher[VERSION]' folder.
- Rename asifont.map that you find there as 'old asifont.map'.
- Copy the newly unzipped asifont.map file into that same folder.
- Relaunch Sequencher.
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 -> Sequences command.
How do I share Sequencher Windows and Sequencher Macintosh 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 version 4.0 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). However, Sequencher 5.0.1 can not open 3.x project files. The message 'The file "<project>.SPF" is not a valid Sequencher project. Try opening another project.' will be displayed.
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?
Click Here. (To read and print this document, you will need the free Adobe Acrobat Reader.)
Does Sequencher import FASTA aligned files?
Yes. Starting with Sequencher 4.10.1, we added the ability to import aligned FASTA files as contigs.
Does Sequencher import Vector NTI files?
Yes. Starting with Sequencher 4.9, MA4 files with all of their associated features can be imported. Starting with Sequencher 4.10.1, Contig Express files can also be imported along with their associated features, quality scores, and trace data.
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.
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.
