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:

Part 1: Basic Features. This part shows you Aligner's main functions, and can be done in Demo mode, without requesting a trial license. It demonstrates how to call bases with Phred, trim ends, vector screen, assemble, and edit.
Part 2: Importing, Exporting, and Saving. This part first shows how to request a fully functional, time-limited trial license that you need for this second part of the tour. It then shows how to add sequences and assemblies to Aligner projects, how to save Aligner projects, and how to export sequences and entire projects.
Part 3: Analyzing Heterozygous Mutations. This part describes how to find and analyze heterozygous mutations in CodonCode Aligner - heterozygous point mutations as well as heterozygous insertions and deletions ("indels").

This quick tour is available online at http://www.codoncode.com/aligner/quicktour/. 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

Aligner Home Page - Next: Opening Aligner Projects