CodonCode Aligner is a leading software program for DNA sequence analysis. Widely used in evolution research, biogeography, and other biomedical fields, it offers many features not found in competing programs, including the ability to compare contigs with ClustalW and muscle, trace sharpening, roundtrip editing, and base calling with PHRED, as well as standard features like assembly, trace and contig editing, end clipping, and mutation detection. The download is a demo version where most features except saving and exporting are fully functional. First-time users automatically get a 30-day trial period where all features are fully functional.
Note: Version 5 requires a new license key. Version 5 is a free upgrade for all users with a current update and support agreement as of March 27, 2014. This includes all users who purchased a license within the past 12 months. Users qualifying for a free upgrade will receive a new license key by email. If you have questions about your license key or support agreement, or would like to provide feedback, please contact CodonCode's support team.
Bug fixes and improvements:
- Sample information dialogs now show base composition and quality summaries
- Accuracy improvements in methylation analysis
- When stretching ABI raw data for methylation analysis or display, failure are now recognized, and lane shifts are partially corrected
- Fixed a bug that changed sample order in contig view printouts
- Adding samples to existing alignments sometimes led to wrong offsets fixed
Known Issues:
- Updating contigs in roundtrip editing fails if any of the samples or contigs has unaligned ends; to avoid this problem, use ClustalW to generate the contigs for roundtrip editing
- Aliases (shortcuts) to files do sometimes not work properly, for example when selecting multiple files
- In the PDF version of the documentation, many bookmarks in the text are slightly wrong -
- clicking on a link in the text will move to the page just before the correct page
- File names with special characters may cause problems when imported using "Import -> Add Folder" on Windows (they can be imported using "Import -> Add Samples")
- On Windows, going to the menu without selecting anything can result in the keyboard being ignored in Aligner (due to a Java bug); if this happens, just click any open Aligner window to select something
- On some OS X versions, the keyboard shortcuts for inserting gaps are shown incorrectly as tabs. The actual shortcuts are "space" and "shift-space".
