Sci Ed Software
Software for the Molecular Biologist

Frequently Asked Questions

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Installation, Evaluation - Clone Manager 10

Clone Share

General Topics

File Handling

Help File


How do I install an evaluation copy of Clone Manager 10?

Click on the link on the Home page or on the product description page to download the installer and run it on your computer. This will install the Clone Manager program and shortcuts on your desktop and the start menu. Double-click to open Clone Manager. Follow the prompts in the License Manager wizard to configure Clone Manager as a 30-day trial evaluation license and select the Professional or Basic edition to evaluate.

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What is the difference between the Professional and Basic editions?

Both editions provide molecule viewing graphic maps and cloning operations. The Professional edition adds primer and alignment operations as well as designing primers for cloning methodologies that involve PCR amplification.

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I am evaluating the Basic edition. How can I see what the Professional edition can do?

You can try the other edition by clicking File, License Clone Manager. The dialog will show what license you are currently evaluating. Click the Manage button to run the License Manager wizard and select the option to change your evaluation license.

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What happens when the evaluation license expires?

When your evaluation license is close to expiring, the title bar of Clone Manager will update to give you a reminder. When the evaluation license expires, your use of Clone Manager will be limited to license management and the file converter dialog. The file converter will enable you to export any of the molecules you created so that you can use them in another program.

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How do I buy the program?

If you have been running an evaluation copy of Clone Manager, click File, License Clone Manager. Verify the trial license you installed and then click the Buy link to go to our website page that has a link to the on-line cart where you can enter your purchase details. Once your purchase is complete, you will receive an email with the details of your license. If you have not installed an evaluation copy, click on the product description page for Clone Manager Professional or Basic and review the license types available and costs involved. Click on a link on the description page when you are ready to make a purchase.

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How do I install my new Clone Manager license?

Run the Clone Manager program and click File, License Clone Manager. On the status dialog, click Manage and select the option to Activate your license. You will need the license number and password that you received in the email confirmation of your purchase. Enter the license details and note that your license has been activated.

If you did not install an evaluation copy of the program, you should do that now and then activate the license, using the information above.

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How do I register my license?

Run Clone Manager and click File, License Clone Manager. Click the link to Register your license and complete the registration form. It is not necessary to register your license but it is a good idea. Registration will identify you as the license holder and you will be able to retrieve your license number and password in the event that they get lost. Should you encounter a situation where additional support is needed, we will need to be able to access your license record. We do not use this information for marketing purposes and follow applicable data protection laws.

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How do I move my license to a new computer?

You will need the license number and password that you received in the email confirmation when you purchased your license for Clone Manager. On your old computer, run Clone Manager and click File, License Clone Manager. Click Manage and select the option to transfer your license to a new computer. Confirm this action and note that your license has been successfully removed. Close Clone Manager and uninstall if desired.

On your new computer, download and install Clone Manager. Run Clone Manager and click File, License Clone Manager. Click Manage the select the option to Activate and enter your license details. You can move your license up to three times. (If you need to frequently move your license, you may want to consider an alternate license type, such as a network concurrent license.)

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How do I run Clone Manager as part of a concurrent license group?

Install Clone Manager on your computer (see above). Run Clone Manager and click File, License Clone Manager. Select Join a Concurrent License Group. For most users, the auto- discovery mode will work without any effort. However, if you have a more complex network environment, you may need to ask your administrator for the details you should enter here. You can also use the License Clone Manager wizard to leave a concurrent license group, when needed.

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What is Clone Share?

Clone Share is a companion program to Clone Manager. The Clone Share program runs as a web server application on a central network server or a local lab computer. It facilitates the sharing of molecules between multiple users running Clone Manager.

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Why would I run Clone Share?

Clone Share is useful if you have several users that need to share the same molecules. It is most convenient when you have a collection of important reference molecules that all of your people use. It also makes possible the sharing of molecules between research groups who are not located at the same physical site or within the same local network.

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Do I need to update to Clone Manager 10.1 to use Clone Share?

Yes, version 10.1 is needed to access the Clone Share companion application. This is a free update for users of Clone Manager 10.0 (Clone Manager 9 users can purchase an upgrade). Open the Downloads section and click the button CM10Setup.msi to download and run the installer. It will automatically update your version (administrator privileges required). All of your settings will be retained, including your current license information.

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Can I use Clone Share with Clone Manager version 9?

No, Clone Manager version 10.1, or newer, is required to access Clone Share. For information about upgrading Clone Manager, please visit

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How can I upload molecules to Clone Share?

Individual molecules can be saved using the menu: File, Clone Share, Save to. To upload a number of molecules you can use the Multiple File Converter utility located on the menu File, Tools.

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How can I move several molecules to a new folder within my Clone Share?

You can select several items by holding down the control or shift keys when you click an item. Multiple selected items will show a highlight bar on the item’s name. You can now right click one of the selected items and select the move option. This multiple selection method also works if you need to delete several items.

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Does Clone Manager work with Windows 10?

Clone Manager 10 and the last version of Clone Manager 9 (version 9.51) fully supports and is fully tested on the Windows 10, Windows 8, and Windows 7 operating systems. If you are still using Clone Manager 9, you can download a free incremental update to bring your software to version 9.51.

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Does my Clone Manager license expire on a specific date?

No, your Clone Manager license does not expire. You can continue to use your Clone Manager software for as long as it is useful to you. Technical support is available by email or telephone without additional cost.

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Access to the NCBI web site seems to have stopped working. What can I do to continue to use Clone Manager with Entrez or BLAST?

NCBI has changed the URL used to reach the web site (going to a more secure https link) and is phasing out the use of sequence GIs as sequence identifiers.

Clone Manager 10 and the last update to Clone Manager 9 (version 9.51) has the changes necessary to allow you to continue to use the Retrieve from Entrez (E-utils), Browse Entrez and Search, and BLAST internet search functions. If you are still using Clone Manager 9, you can download a software patch that will update your program to version 9.51.

If you are using earlier versions of Clone Manager, you can use the Entrez web site directly to find molecules of interest. Download molecules files to your computer in GenBank format and then later open the files with Clone Manager for further use.

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How can I paste a molecule into the new version of Clone Manager?

On the File menu, click Other Tools, Import from Clipboard to paste molecule data into a new molecule structure in the Clone Manager program.

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How can I copy my sequence to the clipboard in FASTA format?

With the molecule open in the molecule viewer window, click Tools, Export, Export Molecule Data. Set the option to FASTA in the upper section and set the option to Copy to the Clipboard in the lower section. Click OK. Your sequence data is now on the clipboard in FASTA format, ready to paste into another application. FASTA is a very simple format that is the required format for many sequence analysis programs, especially over the web.

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What's the easiest way to prepare a group of files to share with others?

You can use the multiple file conversion utility to convert a batch of files in Clone Manager format into the standard GenBank format, all in one easy step. Click File, Other Tools, Multiple File Conversion to get started. You can identify the files or folders of files to convert and specify the location (folder) where you want the program to save the files, and you can select the format to convert to. Files converted to the Compact GenBank format will contain essential molecule data in a format that is consistent with the standard GenBank file format and can be shared with others who do not use the Clone Manager program.

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How can I read in more/different features when importing a GenBank file?

If you are using a recent version of Clone Manager, you can identify the feature keys that should be imported when you open a file in standard GenBank or EMBL format. Just click File, Preferences, then the Import Features tab. Click the Add button to include a new feature key on the import list and select the Draw As feature type to tell the program how to display this feature in Clone Manager. (Note: complex features consisting of joins not supported in versions earlier than 9.2.)

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Can Clone Manager read in GenBank features with joins?

The latest versions of Clone Manager (ver 9.2 or later) adds support for GenBank joins (segmented features). If you routinely retrieve GenBank files that contain joins, you will want to change your import filter at this time. (If you do not change the import filter settings, Clone Manager will read in the CDS features with joins as well as the exons for each feature, resulting in maps with apparent duplicate features.) To change your import filter, click File, Preferences, Import Features. Select the feature key Exon, click the Edit button, and change the Draw As style from Gene to Info only.

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How can I see the basepair positions for join segments?

When viewing the Features display in the molecule viewer window, you can move the mouse over the small symbol to the left of the feature name. The cursor charges to a rectangle shape and you can click with this cursor to open a popup box that shows the location (basepair positions) for the feature segments and feature qualifiers. Click outside the popup box to dismiss. When viewing the Map, click on the feature to select (yellow highlight shows extent of feature) and then click the Properties toolbar button to see the join basepair position information. Click on any enzyme site to reset the right panel to the enzyme site list.

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My GenBank file has features with the Regulatory key. How can I read these into Clone Manager?

Clone Manager has a list of feature keys supported in GenBank/EMBL file formats and support for mandatory qualifiers. You can modify your list of feature keys that should be imported when you open a file in standard GenBank or EMBL format. Click File, Preferences, then click the Import Features tab. Click the Add button to include a new feature key in the designated features list. When the dialog box appears, select the Regulatory key from the list. Then select the Draw as Type to tell the program how to display this feature in Clone Manager.

If you select Region as the Draw as Type for Regulatory features, you will be able to see the features on your map and on the features table. You can later change small regulatory features to Labels or less important ones to Info Only if your map becomes cluttered. To change the drawing style for an individual feature, select the feature on the Features tab and click the Edit toolbar button.

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How do I use the Clone Manager Help system?

Click on the main toolbar Help button (far right) to open the Help system. Click on a category in the list provided to navigate to information within that category. For more specific help questions, click the Show button in the Help window toolbar to open the search pane on the left. Type in a keyword related to the help needed and click the List topics button. Then select the topic to display and click the Display button. Click the Hide button to close the search pane.

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I just downloaded a new Clone Manager help file and it doesn't seem to be working. What do I need to do?

Windows security updates can enable a block that will prevent the display of compiled help (*.chm) files you download from the internet. You may need to unblock this help file before use. In Windows Explorer, right-click on the Clone Manager help file you just downloaded and select Properties from the menu. Click the Unblock button (lower right) on the General page and then click Apply. If you do not see the Unblock button, you may need to log on as administrator.

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I'm getting an error message when I try to access Help in the network version of Clone Manager. How can I read application Help topics?

Security updates for Windows operating systems have introduced new security features that interfere with the operation of compiled HTML help files (*.chm) accessed across a network. "Action Canceled" or "Page cannot be displayed" error messages will appear in place of help topics in the Help viewer window.

Recent versions of Clone Manager can access HTML Help files on local computers, in place of help files in the network program installation directory. Ask your network administrator to make the compiled help file CM10Help.chm (CMSuite9.chm or Clone9.chm for version 9 software) available for you to copy to your home directory. (In Clone Manager, click File, Preferences, Basic to identify the location of your home directory, if needed.)

Once the help file is placed in your home directory, you can start Clone Manager and use the Help button within the Clone Manager program.

You can also download a new help file from this web site, if needed. In the Downloads section, click on Clone Manager User Documents and select the appropriate help file. You may need to unblock this file after download. Please follows the instructions on the download page.

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How can I export the sequence of a primer I've just designed?

With the primer open in the primer viewer window, click the Info tab and then click the toolbar button Export Primer Sequence. Select the option to export the primer sequence to a disk file or to copy the primer sequence to the Windows clipboard so that you can paste the primer sequence into another application. If your primer is a part of a primer collection, just open the Primer List and select (highlight) this primer in your collection. Click the toolbar button Export Primer Sequence and select to export to a disk file or copy to the clipboard.

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What's the quickest way to create a PCR amplified product?

In Clone Manager Professional, click Primer, Create Product to create a new DNA molecule that is the amplified product of a PCR-type reaction using two primers and a DNA molecule that you specify. Select the molecule and then select the two primers and click OK. If an amplified product can be produced, the results screen will show the product size, GC content, melting temperature and annealing temperature. You can select to use the new molecule now, save it to disk for later user or export the product sequence as a text file.

If an amplified product can not be produced using standard PCR reaction conditions, you can opt to relax these conditions and try again. If more than one product is possible, you can opt to open the Analyze Mix Wizard to view the more detailed results and then use the Create Product toolbar button in the results section to create the product of interest.

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How can I import a primer collection?

In Clone Manager Professional, you can use the Import option to create a primer collection by reading in primer data contained in a tab-delimited text file prepared in another application. Open the Primer List and click My Collections. Click the first toolbar button (Folder Options) and select Import. In the import module, select the text format file that contains your primer data. Follow the screen prompts to identify the data in each column and the first row to start importing.

Preparing data for import -- If your primer data is in an Excel worksheet, for example, you can open the worksheet in Excel and use Save As... to save your file in Text (tab delimited) format.

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