CodonCode Aligner
CodonCode Aligner


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CodonCode Aligner free download for Mac

CodonCode Aligner

28 August 2017

Analyze DNA sequences.


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.

What's new in CodonCode Aligner

Version 7.1.2:
  • Changes to assembly and alignment preferences were not saved
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"
CodonCode Aligner for Mac Old Versions

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