CodonCode Aligner - A Quick Tour

This Quick Tour will show the most important features of CodonCode Aligner. It takes about an hour or two - time that can easily save you many hours later. Some of the features shown are unique to CodonCode Aligner, so we suggest that you take the entire tour (or at least the first two parts, if you will never use the mutation detection features).

The tour is divided into three parts:

This quick tour is available online at If you downloaded and installed CodonCode Aligner, a copy of this tour has been installed in your installation directory as an Adobe PDF file named "QuickTour.pdf".

Part 1: Basic Features Part 2: Import, Export, Save Part 3: Finding Mutations
Aligner Projects Obtaining a Trial License Finding Point Mutations
Base Calling To Assembly Creating New Projects Defining the Coding Region
The Contig View Adding Sequences and Assemblies Specifying Where To Search
Navigating Exporting Sequences and Projects Finding Heterozygous Indels
Editing   Analyzing Heterozygous Indels
Copying Sequences   Exporting Results
Using Online Help    


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