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CodonCode AlignerPhredPhrapConsedPolyPhredTraceViewer |
This page shows screen shots of CodonCode Aligner, our tool for sequence assembly, editing, and mutation detection for Windows and Mac OS X. To see CodonCode Aligner in action, please visit the Tutorials page. Project view - Feature view - Contig view - Preferences - Trace view - Base view - Quality overview The project window shows the contents of projects:
CodonCode Aligner lets you define regions of interest or "Features", which can be shown in table form. The example below shows features in a mutation detection project:
Double-clicking on a feature will bring up the corresponding contig view and trace view: The contig view shows the contents of assembled contigs:
The background colors indicate the sequence qualities. Colors (and many other things)can easily be customized to follow one of several familiar color schemes in the Preferences:
You can view and edit sequence traces in the trace view window:
Or you can view sequences in the base view window (here shown with a different color scheme):
You can get use the quality overview to quickly navigate to low-quality regions:
There are many other things you can do, including end clipping, vector trimming, assembling, running Phred for base calling and Phrap for assemblies, exporting sequences or entire projects, ... If you are interested, download the demo version, and then request a time-limited trial key. |
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