CodonCode Aligner

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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.

The initial purchase includes one year of free updates and support. Yearly extensions of the update and support period are available.

Academic Prices

Academic licenses are for researchers at universities and non-profit institutions, and may not be transferred to or used at for-profit institutions.

$960
  • Additional academic single-user license 
$720

Academic licenses include licenses to use the workstation versions of Phred and Phrap free of charge.

Business Prices

The following prices are for customers at for-profit companies:

$1920
  • Additional single-user license 
$1440

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

Annual Maintenance Option

The initial license includes one year of free updates and support. After one year, you have the option to extend your update and support period by 12 months by paying an annual maintenance fee:

  • Annual maintenance for first academic license
$240
  • Annual maintenance for each additional academic license 
$150
  • Annual maintenance for first business license
$480
  • Annual maintenance for each additional business license 
$300

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.

Purchasing Aligner Licenses

Before buying, please make sure that CodonCode Aligner fills 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 to request a quote, and let us know how many single-user licenses you would like to buy.

The fastest way to buy is by using a credit card; we will send you our credit card authorization for when we send you a quote.

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

  • You send us a copy of your purchase order, preferably by fax to (+1) 781 407-0807). Also, please let us know the computer ID(s) (as reported by CodonCode Aligner) for the computer(s) you would like to use the software on.
  • 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.

Single User Licenses

CodonCode Aligner licenses are single user licenses. For each single user license you purchase, you can receive one install key, which allow use of CodonCode Aligner on a specific computer.

If you plan to use CodonCode Aligner on different computers, you instead request a license server license.

License Server License

The License Server licenses allow you to install CodonCode Aligner on an unlimited number of computers, but limit the number of concurrent users to the number of licenses you purchased.

The License Server for CodonCode Aligner is a separate program that is installed on one computer that acts as the license key server. Other computer that want to run Aligner can check out keys from the License Server over the network. The 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 license server licenses is the same as the price for Single User Licenses.

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, and then request the key by sending the "computer ID", as reported in the license dialog, 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, or replace the hard drive on your 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.

Other Licenses

We also offer site licenses and license packages for entire departments and universities. Prices depend on the number of concurrent users and install keys. For a custom quote, please send email to:

All sales are subject to CodonCode Corporation's software license agreement that is displayed when you install CodonCode Aligner. A printable copy of the license agreement for CodonCode Aligner can be found inside the folder where you installed CodonCode Aligner.

Academic discounts are granted solely at the discretion of CodonCode Corporation. CodonCode Corporation reserves the right to determine if a purchase qualifies for academic prices.