Abstract Advancements in high-throughput nucleotide sequencing techniques have brought with them state-of-the-art bioinformatics programs and software packages. Given the importance of molecular sequence data in contemporary life science research, these software suites are becoming an essential component of many labs and classrooms, and as such are frequently designed for non-computer specialists and marketed as one-stop bioinformatics toolkits. Although beautifully designed and powerful, user-friendly bioinformatics packages can be expensive and, as more arrive on the market each year, it can be difficult for researchers, teachers and students to choose the right software for their needs, especially if they do not have a bioinformatics background. This review highlights some of the currently available and most popular commercial bioinformatics packages, discussing their prices, usability, features and suitability for teaching. Although several commercial bioinformatics programs are arguably overpriced and overhyped, many are well designed, sophisticated and, in my opinion, worth the investment.

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If you are just beginning your foray into molecular sequence analysis or an experienced genomicist, I encourage you to explore proprietary software bundles. They have the potential to streamline your research, increase your productivity, energize your classroom and, if anything, add a bit of zest to the often dry detached world of bioinformatics. ,,, INTRODUCTION Most mornings I wake up to a slew of spam email from biotech companies offering unbeatable bargains on next-generation sequencing (NGS). Yesterday, for example, Beckman Coulter kindly offered to ‘take the stress out of sequencing’ for only a few thousand dollars. Illumina recently provided me with ‘a glimpse into the future of genomics’, just by clicking on their buyer’s guide. And Macrogen, a South Korean sequencing conglomerate, dared me to race the HiSeq ‘Xpressway to the $1000 genome’. These irritating emails underscore an important point: massively parallel sequencing has arrived to the masses.

NGS is now standard fare in almost all facets of life science research []. It is also big business and intimately tied to another burgeoning industry—bioinformatics [].

Anyone who has ever had something sequenced, such as a genome, transcriptome, gene or PCR product, or used nucleotide or protein sequence data in their research has probably dabbled in bioinformatics. Not long after scientists started generating molecular sequence information, computer-savvy biologists and biology-savvy computer scientists began developing programs to analyse those data []. Given the breadth and depth of questions that can be addressed with primary biological sequence information, many of these programs have become immensely popular. For example, the journal article describing the basic local alignment search tool (BLAST), which allows a query nucleotide or amino acid sequence to be compared against a database of sequences, has been cited >50 000 times []. Today’s omics-obsessed scientific marketplace is overflowing with bioinformatics programs.

Whatever your sequence analysis problem (assembling, aligning, annotating, folding, etc.), there is probably a program or online application to solve it—skim through the community-maintained list of bioinformatics software at SEQanswers.com to see what I mean:. The majority of these tools are open source, but they can be difficult to learn, install and run; some require an in-depth knowledge of computers [].

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There are, however, various commercial alternatives, which bring together multiple bioinformatics programs into user-friendly stand-alone packages. Although beautifully designed, these software suites can come with a hefty price tag, meaning that most researchers, teachers and students are lucky if they can afford just one. Like buying a car, choosing between different suites can be challenging, and there is surprisingly little information appraising the different programs. Here, I describe my own experiences with using commercial bioinformatics packages, focusing on their cost, functions and educational utility. I have no affiliation, past or present, with any of the programs, software or companies described in this manuscript, but being a longtime genomics enthusiast, I use many of these applications daily, and I am a strong proponent of ease of use and accessibility in bioinformatics []. Although the focus of this article is commercial software, there are a number of free browser-based bioinformatics toolkits worth considering, e.g. Two toolkits that I use regularly and recommend are MEGA [] and Unipro UGENE [].