As well as its assembly algorithms, Sequencher includes not one but two multiple-sequence alignment algorithms, Clustal and MUSCLE. A multiple sequence-alignment or (MSA) is not the same as  sequence assembly so don't be surprised if your contigs and multiple-sequence alignments look different. The algorithms which produce them are doing different tasks.

Mitochondrial DNA Typing

The forensic version of Sequencher gives you special functions for DNA-based identification. Using Sequencher’s Templates, which can help to support your standard operating procedures, you ensure your analysts are all using the same parameters and settings in their projects. We have even provided you with the Cambridge Reference Sequence (rCRS) as an example template in every installation.

Differential Expression

The end goal of RNA-Seq analyses for many is differential expression. The best tool is Cufflinks, a suite of peer-reviewed algorithms found in Sequencher. In its simplest form, this is a four step process which takes you from re-alignment to differential expression by way of normalization. All of the steps are carefully presented through graphical user interfaces with access to command-line options but without going through the command line itself. The suite can deal with replicates and different experimental samples or conditions.

Microarray Expression

With more than a decade of commercial availability behind them, microarrays are still a popular method of gene expression profiling despite the increasing popularity of RNA-Seq. Whether you are working with microarrays looking to re-analyse pre-existing results or trying to perform concordance studies with RNA-Seq, CodeLinker is the tool to answer all your needs. CodeLinker uses the metaphor of the experiment for each analysis or step.


Over the last few years, RNA-Seq has become an immensely popular technique its own right as an adjunct to microarrays in gene expression studies. The ability to sequence RNA and align it prior to further analyses is a powerful but technically challenging technique. This is largely due to the fact that the powerful sequence aligners are all command-line driven. Sequencher gives you a consistent graphical user interface across its NGS algorithms and access to all the options that you would normally see on the command line.


When you are working with NGS data, whether it is DNA-Seq or RNA-Seq, you will want the best algorithms. For speed, BWA-MEM is able to give you reference-guided alignments with genome sizes up to human genome size and beyond. Despite its speed, it still has a small memory requirement. For a feature-rich program able to deal with regular sequences, spliced sequences, methylation-tolerant alignments, SNP-tolerant alignments,  and RNA-I tolerant alignments, then GSNAP is the algorithm of choice.


Sequencher has built its reputation on proprietary DNA sequence assembly algorithms that have set the standard in research labs across the world for over 25 years.  No other program gives you such a comprehensive set of science-driven features that can fit almost any project and get results fast. 

Sequencher has several different assembly algorithms as well as different assembly modes providing the flexibility to work with any of kind sequence data.