CodonCode Corporation
Better Software for DNA Sequencing

CodonCode Aligner Tutorials

From this page, you can view tutorials for CodonCode Aligner.

Use the navigation buttons directly below for quick access, or browse all the individual tutorials futher down the page.

 

Recommended for new users:

Introduction to Aligner Video

This video gives a brief introduction to CodonCode Aligner. It shows some basic functions, including sequence assembly and alignment.

Quick Tour Video

The quick tour shows some basic features of Aligner. Make a new project, import samples, end clip, assemble, and look at some editing functions.

How To:

Assemble in Groups Video

A video explaining how to assemble samples based on the sample's names, creating one contig for each group.

Compare Contigs Video

Learn how to compare contigs to each other, and then go back to the underlying traces to verify differences.

Start Blast Search Video

Watch this video to see how to start BLAST searches for sequences directly from within CodonCode Aligner.

Restriction Cloning Video

This video explains how to simulate a restriction cloning experiment, and how to verify the clone reading frame.

Gibson Assembly Video

A video showing how to use the Gibson Assembly cloning feature in CodonCode Aligner.

Primer Design Video

Follow along to see how to design sequencing and PCR primers, and how to use them in your Aligner projects.

Restriction Map Video

This video explains how to use restriction maps and how to generate virtual gels in CodonCode Aligner.

RFLP Analysis Video

Learn how to use Aligner's restriction fragment length polymorphism analysis feature.

Import Matches Video

See how to import only those sequences that have matches with a chosen reference sequence.

Using Reference Sequences Video

A video on how to use reference sequences to bridge gaps and set the sample orientation during alignments.

Shorten Reference Sequence Video

Learn how to automatically shorten reference sequences as needed when creating alignments.

Tips:

Quality-based Consensus Video

Learn how a quality-based consensus can significantly reduce the amount of editing you need to do.

Aligner in Evolution Research Video

Watch this video to see useful features for evolution research, including aligning and comparing contigs to each other.

Customize Toolbars Video

A tutorial that shows how to change the toolbar display, and add or remove items from toolbars in Aligner.

Match Consensus Video

This video explains how to use the "Match Consensus" feature to quickly and automatically edit areas of low quality sequences.

Roundtrip Editing Video

Learn how to export a contig, edit it in a different contig editor, and reimport & update the contig in CodonCode Aligner keeping the link to the underlying traces.

Tips Video

See tips for using Aligner, like mask bases, highlight discrepancies, reverse complement, move gaps, copying, minimize editing, and unaligned ends.

Aligner License Server:

Server Set Up Video

This video explains how to get started with the License Server. See how to set up and configure your server.

Using the License Server Video

Learn how to use the Aligner License Server from CodonCode Aligner to get (and return) license keys.

New Features added in recent CodonCode Aligner versions:

New in Aligner 12 Video

This video shows some new features in Aligner 12.0: Transferring tags between sequences, annotation display in the contig view for aligned samples, and TA cloning.

New in Aligner 11 Video

Watch some new features in Aligner 11.0: Simulate Gibson Assembly, synchronize sequence starts, and automatically find and annotate common features in samples.

New in Aligner 10 Video

Learn about a few main new features in Aligner 10.0, like using sequence maps with feature annotations and enzyme cut sites, virtual restriction cloning, and separating alleles.

New in Aligner 8 Video

See what is new in Aligner 8: Amino-acid based alignments, dot plots for visual sequence comparison, and NGS tools to cluster and identify new sequences.

New in Aligner 5 Video

Have a look at Aligner 5 which introduces alignments with Bowtie2, moving gaps with drag & drop, seeing paired ends, and printing the contig overview.

 

For additional information about specific features, you can use the help available within CodonCode Aligner ("Help" menu -> "Aligner Help..."). This help is also available as a PDF file, which is installed automatically in the same folder where CodonCode Aligner is installed.

For help with mutation finding in CodonCode Aligner, please visit www.codoncode.com/aligner/quicktour/snps.htm (please note that this help is slightly outdated, so some dialogs etc. may look different in current CodonCode Aligner versions).