Note that this is a beta version - it has not been fully tested, and may contain bugs and partially implemented features.
This version requires new license keys (unless you received a new license key within the past 2 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:
- Sequences can be downloaded by accession number from GenBank
- New text sequences can be created from the file menu
- Amino-acid translations can now be use to set background colors, and can also be viewed instead of nucleotide bases
- In the Contig view, the top panel can now alternatively show the overview (as before) or a "variation" table
- 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