Prices for CodonCode Aligner Licenses

Prices for CodonCode Aligner licenses depend on the number of licenses bought, and where the licenses will be used.

Customers at universities and non-profit institutions, including government-funded research labs, usually qualify for academic prices. Academic prices reflect a 50% discount relative to the business prices. All prices are in US dollars.

Academic and business licenses are perpetual - they do not expire. The initial purchase includes one year of free updates and support. Optional yearly extensions of the update and support period are available. Customers with expired update and support agreements can purchase upgrades to the current version.

Academic / Government Prices

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Single user license
Concurrent license

Single user licenses are bound to one specific computer. Concurrent licenses (also called "License Server" or "network" licenses) can be used on multiple computers on an alternating basis, and are managed by the Aligner License Server program. Both license types are the same price.

Academic licenses are for researchers at universities and non-profit institutions, and may not be transferred to or used at for-profit institutions. Academic licenses include licenses to use the workstation versions of Phred and Phrap free of charge.

Business Prices

Business licenses are perpetual licenses for customers at for-profit companies.

Request a quote
Single user license
Concurrent license

Single user licenses are bound to one specific computer. Concurrent licenses (also called "License Server" or "network" licenses) can be used on multiple computers on an alternating basis, and are managed by the Aligner License Server program. Both license types are the same price.

Business prices do not include licenses for Phred, Phrap, or other components of the Phred-Phrap package.

Purchasing Aligner Licenses

Before buying, please make sure that CodonCode Aligner fulfills your needs. If you have not already done so, please download a demo version of Aligner. The first time you run CodonCode Aligner, you will receive an automatic trial license that allows you to test all features of CodonCode Aligner for 30 days.

When you are ready to buy, please request a quote, and let us know how many licenses you would like to buy.

The fastest way to buy is by using a credit card; you can download our credit card authorization form, fill it out and either fax it to us at (+1) 781 417-6400, or upload it to our online dropbox.

If you are using a purchase order, the following procedure applies:

  • You send us a copy of your purchase order, preferably by email to, or by fax to (+1) 781 417-6400. Also, please let us know if you are purchasing single-user license(s) or concurrent license(s). If you are not sure which license type is right for you, please read this post on our support forum.
  • After we receive your purchase order, we will send you an email with temporary license keys that are valid for 60 days, and an invoice in Adobe PDF format.
  • You print the invoice, and submit it to your purchasing deparment for payment. Payment is due within 30 days.
  • Once we receive payment, we send you an email with permanent license keys that replace the temporary license keys.

Please note that sales of licenses for CodonCode Aligner are governed by the terms of the Software License Agreement that is displayed when you install CodonCode Aligner, and also available as a PDF file inside the "CodonCode Aligner" folder and here. The license agreement is non-negotiable - the legal and technical costs of changing license terms would be much higher that the cost of a license, however reasonable a request for changes might be.

If you are ordering from Japan or China you can either order directly from us, or through our official resellers Hulinks Inc. (Japan) or Phdbiotech Inc. (China).

Annual Maintenance Option

12 Months Full Maintenance, Support and Upgrades for FREE with Each License!

Academic and business licenses of CodonCode Aligner are perpetual, which means your licenses do not expire. Your original purchase of CodonCode Aligner includes all updates, upgrades and support FREE of charge for 12 months from the date of purchase. After that, you have the option to extend your update and support period by 12 months by paying an annual maintenance fee:

Annual Maintenance
Per academic license $180
Per business license $360

If you choose to not extend you update and support period, you can keep using your current version of CodonCode Aligner. However, you will not qualify for support, and will have to pay if you want to upgrade to a new version of CodonCode Aligner.

Please note that we can not guarantee that older versions of CodonCode Aligner are compatible with any operating system that is newer than the release date of this older Aligner version.

Upgrading from Old Versions

CodonCode Aligner users with expired update and support agreements can purchase upgrades to the current version, which include 12 months of free updates and support.

Per academic license $360
Per business license $720

Student and Teaching Licenses

Student license $320 US 2 years
Teaching licenses free duration of the class

Student licenses are available to undergraduate students, graduate students, and postdocs. These licenses are valid for two years and just for one user. They are bound to the student as a person and can only be installed and used on one computer. The student licenses can be upgraded to a full license at any time within the two years the student license is valid by paying the difference in price to an academic license.

Teaching licenses are free temporary licenses for classroom use. Click here for more information about our teaching licenses.

License Types: Single User and Concurrent Licenses

Single user licenses are bound to one specific computer. For each single user license you purchase, you can receive one install key. If you plan to use CodonCode Aligner on different computers, you instead request a concurrent license.

Concurrent licenses are intended when you want to share licenses between different computers on an alternating basis. Concurrent licenses allow you to install CodonCode Aligner on on as many Macs and/or PCs as you like on the same network, but limit the number of computers that can access CodonCode Aligner at once to the number of licenses you buy.

Concurrent licenses are managed by a separate program, the "Aligner License Server". The Aligner License Server program is installed on one computer that acts as the license key server. Other computers that want to run CodonCode Aligner can check out keys from the License Server over the network. The Aligner License Server also allows checking out of extended keys for overnight or travel use. For more information about the Aligner License Server, visit the License Server page.

The price for concurrent licenses (also called "License Server licenses") is the same as the price for single user licenses; the Aligner License Server program is provided free of charge if you purchase one or more concurrent licenses.

For more information about single user licenses and concurrent licenses, please read this forum post.

Install Keys

To use CodonCode Aligner, you need a valid license key ("install key"), which is hardware-specific. To obtain an install key, you must first install CodonCode Aligner or the Aligner License Server depending on which type of license you bought, and then request the key by sending the "computer ID", as reportedby the program, to CodonCode Corporation.

For each single user license, you can receive one install key, which allows you to install Aligner on one specific computer. If you need to use the software on more than one computer, you should purchase a License Server license instead of a single user license (the price is the same).

Replacement Install Keys

Occasionally, you may need a replacement install key, for example if you purchase a new computer. Replacement install keys will generally be issued free of charge (within reason). Replacement keys cannot be used when the original keys are still being used - trying to use an original install key and a replacement key will invalidate one or both keys.

Replacement install keys will be issued while you have a current update and support agreement, and for up to two years after your update and support agreement has expired. If you choose not to use the annual maintenance option and need a new license key more than three years after your initial purchase, there will be an administrative fee for each replacement license key issued.



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