CodonCode Aligner for Evolution Research

CodonCode Aligner is a leading program for DNA sequence assembly and alignments. CodonCode Aligner offers unique time-saving features, specifically developed for evolution and population genetic studies, and can dramatically reduce the time required to analyze DNA sequences. Download CodonCode Aligner now, watch the "Evolution" tutorial, or read on.

• Fast:

Group samples by name and assemble contigs for hundreds of samples in seconds.

Generate contigs for dozens or hundreds of isolates or species with a single click of a button. CodonCode Aligner lets you define how to interprete sample names, and automatically groups samples into contigs, based on their names. You can also automatically trim ends, clip vector, and even base call with Phred before assembly.
View the "Assemble in Groups" Flash tutorial

• Accurate:

Minimize manual editing with quality-based consensus sequences.

In other popular sequencing software, you have to edit every single discrepancy, even if one sequence is clearly wrong and the other is clearly right. In contrast, CodonCode Aligner will automatically pick the correct consensus base, using sequence qualities to decide which base is more likely to be correct.
View the "Quality-based Consensus Sequence" Flash tutorial

• Powerful:

Align contigs with ClustalW or muscle; double-click to go back to the traces.

A unique feature in CodonCode Aligner is the ability to build "contigs of contigs" - align contigs to each other, while preserving the ability to go back to the original traces with a simple double-click.

You have the choice between several powerful algorithms for contig sequence alignments - use the popular program ClustalW, the more modern and often more accurate program muscle, or CodonCode Aligner's algorithm - all without the need to export or duplicate sequences.
View the "Compare Contigs" Flash tutorial

• Innovative:

Multiple methods to analyze heterozygous insertions and deletions. View sharpened traces.

CodonCode Aligner offers several methods to find and determine the size of heterozygous insertions or deletions - from "splitting" indels into two pseudo-alles to subtracting reference traces to reveal the mutated trace.

Another innovative feature in CodonCode Aligner, useful even if you never see heterozygous indels, is the ability to view sharpened traces - one of many new features introduced in CodonCode Aligner version 2.0.

• Affordable:

Substantially less expensive than other DNA sequencing software.

The price for an academic license if $720 (US). To enable you to share licenses between many computers, we offer the Aligner License Server at no additional cost.

Details about prices and licensing are available at our "Prices" page.

• Try it!

Download CodonCode Aligner for Windows or OS X, and try it with your own data.

The first time you use CodonCode Aligner, you will automatically receive a 30-day trial that allows you to test all features of the software. No registration required.

To help you get started, watch the QuickTour, the other Flash tutorials, or browse through more than 200 pages of online help that explain in detail how CodonCode Aligner works, and how to adjust settings to your specific needs.

Fast sequence alignments with CodonCode Aligner

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