CodonCode Aligner Tutorials

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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.

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

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

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

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.

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

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.

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.

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