CodonCode Aligner 3.0.1 released

Announcement of new version releases and related information.

CodonCode Aligner 3.0.1 released

Postby Peter Richterich » Mon Mar 30, 2009 10:12 am

CodonCode Aligner 3.0.1 was released on March 30, 2009. Version 3.0 of CodonCode Aligner introduces a number of new features, and offers significantly improved support for larger sequencing projects.

This version requires new license keys (unless you received a new license key within the past 3 months, and you have a current update and support agreement. Version 3 is a free upgrade for all users with a current update and support agreement as of December 30, 2008. If you have questions about your license key or support agreement, or would like to provide feedback, please contact CodonCode's support team.

Here is a partial list of new features and improvements in CodonCode Aligner 3.0:
  • Amino-acid translations can now be viewed instead of nucleotide bases for all samples, and (independently) used to set the background colors
  • In the Contig view, the top panel can now alternatively show the overview (as before) or a "difference" table
  • Sequences can be downloaded by accession number from GenBank
  • New text sequences can be created from the file menu
  • Memory handling on Windows is now automatic, making it much easier to work with large projects
  • Memory use has been reduced substantially, and can be monitored in the project view
  • Limited 454 support: .sff files with up to about 20,000 samples can be imported
  • Substantial improvements in the assembly algorithm for very large projects
  • New "Script" menu and script commands
  • Improvements in FASTA import (removal of leading and trailing gaps when importing contigs) and export
  • Re-organized the "Contig" menu for easier access to advanced assembly and alignment options
  • After assemblies, contigs are now sorted by # of reads before naming
  • A comparison of features in this and prior versions is available here.
Installers can be downloaded from If you are updating from an older version of CodonCode Aligner, please make sure to follow the update instructions on the download page.
Peter Richterich
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