B RIEFINGS IN BIOINF ORMATICS . VOL 16. NO 4. 700 ^709 doi:10.

1093/bib/bbu030
Advance Access published on 1 September 2014

Buying in to bioinformatics: an
introduction to commercial
sequence analysis software
David Roy Smith
Submitted: 25th June 2014; Received (in revised form) : 7th August 2014

Abstract
Advancements in high-throughput nucleotide sequencing techniques have brought with them state-of-the-art bio-
informatics 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 soft-
ware 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, fea-
tures 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. 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, ener-
gize your classroom and, if anything, add a bit of zest to the often dry detached world of bioinformatics.
Keywords: bioinformatics software; CLC bio; Geneious; genome assembly; nucleotide alignment; phylogenetics software

INTRODUCTION Anyone who has ever had something sequenced,

Most mornings I wake up to a slew of spam email such as a genome, transcriptome, gene or PCR
from biotech companies offering unbeatable bargains product, or used nucleotide or protein sequence
on next-generation sequencing (NGS). Yesterday, data in their research has probably dabbled in
for example, Beckman Coulter kindly offered to bioinformatics. Not long after scientists started
‘take the stress out of sequencing’ for only a few generating molecular sequence information, com-
thousand dollars. Illumina recently provided me puter-savvy biologists and biology-savvy computer
with ‘a glimpse into the future of genomics’, just scientists began developing programs to analyse
by clicking on their buyer’s guide. And Macrogen, those data [3]. Given the breadth and depth of ques-
a South Korean sequencing conglomerate, dared me tions that can be addressed with primary biological
to race the HiSeq ‘Xpressway to the $1000 genome’. sequence information, many of these programs have
These irritating emails underscore an important become immensely popular. For example, the jour-
point: massively parallel sequencing has arrived to nal article describing the basic local alignment search
the masses. NGS is now standard fare in almost all tool (BLAST), which allows a query nucleotide
facets of life science research [1]. It is also big busi- or amino acid sequence to be compared against a
ness and intimately tied to another burgeoning database of sequences, has been cited >50 000
industry—bioinformatics [2]. times [4].

Corresponding author. David Roy Smith, University of Western Ontario, London, Ontario N6A 5B7, Canada. E-mail:
[email protected]
David Roy Smith is an assistant professor of biology at the University of Western Ontario, where he studies genome evolution of
eukaryotic microbes. He can be found online at www.arrogantgenome.com and @arrogantgenome.

ß The Author 2014. Published by Oxford University Press.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/
by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use,
please contact [email protected]
 Buying in to bioinformatics 701

Today’s omics-obsessed scientific marketplace running concurrently. I would be desperately editing

is overflowing with bioinformatics programs. and assembling Sanger sequences with Phred, Phrap
Whatever your sequence analysis problem (assem- and Consed [11, 12] while blasting the resulting con-
bling, aligning, annotating, folding, etc.), there is tigs locally against custom databases and annotating
probably a program or online application to solve the output on an ongoing GenBank entry. A chug of
it—skim through the community-maintained list of coffee and I would switch to gene and genome
bioinformatics software at SEQanswers.com to alignments with ClustalW [13] and MAUVE [14],
see what I mean: http://seqanswers.com/wiki/ which were pumped directly into PAML [15] to
Software/list. The majority of these tools are open measure genetic diversity and substitution rates.
source, but they can be difficult to learn, install and A quick blink of the eyes and I was plotting slid-
run; some require an in-depth knowledge of com- ing-window GC contents across entire organelle
puters [5]. There are, however, various commercial chromosomes, all while mainlining a medley of
alternatives, which bring together multiple bioinfor- phylogenetic and tree-building programs, from
matics programs into user-friendly stand-alone pack- MrBayes [16] to PhyML [17] to PAUP [18] to
ages. Although beautifully designed, these software MacClade [19]. And because some of these applica-
suites can come with a hefty price tag, meaning that tions worked only on a PC and others on a Mac,
most researchers, teachers and students are lucky if I had Windows and Apple operating systems running
they can afford just one. Like buying a car, choosing at the same time, with command-line terminals piled
between different suites can be challenging, and on top of graphical user interfaces (GUIs).
there is surprisingly little information appraising ‘There’s got to be an easier, more efficient way of
the different programs. Here, I describe my own doing this’, I would say to myself, as I tossed another
experiences with using commercial bioinformatics empty coffee cup into the trash. Sensing my angst, a
packages, focusing on their cost, functions and edu- colleague recommended that I invest in a commer-
cational utility. cial, cross-platform, GUI-based bioinformatics pack-
I have no affiliation, past or present, with any of age, arguing that it would streamline and simplify my
the programs, software or companies described in work. I was reluctant to take his advice. I felt that
this manuscript, but being a longtime genomics en- paying for such programs went against the spirit of
thusiast, I use many of these applications daily, and I academic research and that using GUI software
am a strong proponent of ease of use and accessibility would weaken my computational skills. However,
in bioinformatics [5]. Although the focus of this after failing for the fourth time to correctly install
article is commercial software, there are a number and run an open-source genome assembly algorithm,
of free browser-based bioinformatics toolkits worth I gave in and bought a user-friendly bioinformatics
considering, e.g. [6, 7]. Two toolkits that I use regu- bundle, and have not regretted it.
larly and recommend are MEGA [8] and Unipro
UGENE [9]. See Vincent and Charette [10] for a Show me the money
succinct but compelling summary of the drawbacks In 2007, with the grant support of my former PhD
of commercial tools and arguments for freedom in supervisor, I purchased my first bioinformatics soft-
bioinformatics. ware package. At the time, there was a small but
strong cohort of commercial options available,
A bioinformatics magic bullet most of which offered a free 30-day trial—a practice
During my PhD I spent hours a day at the computer that, with few exceptions, continues today, although
assembling and analysing organelle genomes. Friends in some cases the trial period has been reduced to 2
and colleagues would poke their heads into my weeks. After testing an assortment of programs,
cubbyhole of an office and recoil at the sight of I decided on Geneious (Biomatters Ltd., Auckland,
my bloodshot eyes and the genomic chaos playing New Zealand), which was first released in 2005 and
out on the high-definition dual monitors that sur- is now among the more widely used cross-platform
rounded me. ‘Dave, how many analyses are you commercial bioinformatics packages (Table 1).
running?’ they would ask, gaping at the mosaic dis- I chose Geneious not because it was necessarily
array of program windows scattered across the better than other software, but because the company
screens. Like any decent genomics junkie, I usually offered, and continues to offer, student discounts.
had half a dozen different bioinformatics applications Seven years ago, I paid approximately $200 (all
702 Smith

Approximate price of a single-user academic license. Prices were taken directly from company websites (as of 1 June 2014) or were obtained by sales representatives sometime between January and June 2014.
Many companies offer a range of pricing and licensing options, and frequently have promo deals. bRuns on the following platforms: Mac (M), Windows (W) and Linux (L). cCan store, organize and analyse
suitability

(e.g. assemble or map to a reference sequence) next-generation sequencing data. In some cases, de novo assembly features are missing. dContains some tools for studying molecular evolution, such as those for
Teaching
prices in US dollars) for a student license of
Geneious, which allowed me to install the software

5
3
3

3
3
3

3
3
on a single computer. As Geneious increases in
popularity, so does its price tag. As of May 2014, a

performing multiple sequence alignments, phylogenetic analyses and/or repeat identification. eIs able to connect and interact with online sequence databases, such as GenBank. 3 ¼ yes, 5 ¼ no
Workflows student license costs $395 (a standard academic one is
$795), which still makes it among the least expensive

5
5

5
5
5
3 all-in-one commercial suites on the market. In com-
3

3
3

3
parison, stand-alone academic licenses of the
Plug-ins

Lasergene Genomics Suite (DNASTAR, Madison,

USA) and Sequencher (Gene Codes, Ann Arbor,
5

5
5

5
3

3
3
3

3
USA) are around $6000 and $2500, respectively
searchinge

(Table 1).
Database

I have since gone on to test, and in some instances

purchase, a multitude of other commercial bioinfor-
5

5
3

3
3
3
3

3
3
matics platforms, which have varied widely in price,
usability and quality. In several cases, the costs of
Evolutionary
Table 1: Examples, features and comparisons of some commonly used commercial bioinformatics software suites

analysesd

these software suites were not listed on the company

websites or anywhere else online. To get pricing
details, I had to request quotes from sales represen-
5

5
3
3
3
3
3
3

3
3

tatives. For example, after a successful 30-day trial of

analysesc

CLC Genomics Workbench (CLC Bio, Qiagen,

NGS

Aarhus, Denmark), I filled out an online pricing re-

5

5
3
3
3

3
3
3
3
3

quest form and was contacted 2 days later by a sales

agent who provided me with a formal quote (an
Platformb

estimated $5500 for a standard academic license).

M, W, L
M, W, L

M, W, L
M, W

M, W

M, W

I went through similar processes to get pricing on

W

W
M

Lasergene, Sequencher and various other bioinfor-

matics programs. Since starting this article, CLC
Free trial

bio now posts some of their prices online (www.

(days)

clcbio.com; accessible through the ‘buy online’

30
30
30

30

30
30
20

35
14

21

icon), but many companies still require potential cus-

tomers to contact sales reps, making it difficult and
Cost (USD)a

time-consuming to compare prices of different soft-

ware packages. On a number of occasions, after re-
$4049
$4500

$2500
$5500

$5950

$600
$300
$720

$795
$295

questing quotes or free trial access, I was bombarded

with emails and phone calls by sales agents asking
Strand Scientific Intelligence

whether I had come to any decisions about purchas-

ing the software or whether I needed more informa-
tion; one time a representative even called a
Life Technologies
ClC bio, Qiagen

laboratory where I used to work, asking for my cur-

Gene Codes
CodonCode

Softgenetics

rent contact details—so if you request a quote, be

Biomatters
DNASTAR
Company

MacVector
Genamics

prepared to be pestered.

What do you get for your money and for

CLC Genomics Workbench

how long?
MacVector & Assembler

Purchasing a commercial sequence analysis suite is

Genamics Expression
CodonCode Aligner

Full Lasergene Suite

VectorNTI Advance

not as simple as a one-time payment followed by a

lifetime of bioinformatics bliss. There can be hidden
Avadis NGS

Sequencher
NextGENe
Software

unexpected costs and clauses associated with running

Geneious

the software and continuing to use it in the future.

Most commercial packages include 12 months of free
a
 Buying in to bioinformatics 703

maintenance, upgrades and support. Shortly after I for instance—your bioinformatics package might
bought my student license for Geneious, the firm have to be upgraded as well. Most bioinformatics
released a new version of the software. Because this companies offer their software for both Windows
occurred within 1 year of my purchasing the pro- and Apple platforms, and some, including
gram, I was able to upgrade to the newest version Geneious and CLC bio, have Linux versions too,
for free. Geneious and other bioinformatics manu- so in most cases, it is possible to switch operating
facturers have recently switched to ‘version-based systems completely and continue running the
licensing’, meaning that users receive free updates program.
for their version of the software (e.g. switching Things get even more complicated when purchas-
from v1.1 to v1.2), no matter when they are ing network (or ‘floating’) licenses of bioinformatics
released, but access to newer versions (e.g. switching programs. Unlike a single computer license, which
from v1 to v2) requires an upgrade, which typically works only on one computer, a network/floating
costs anywhere from 25 to 75% of the software list license allows multiple people to use a bioinformatics
price. package simultaneously by logging on to a network
Last year, for approximately $6000, I purchased as computer (e.g. a powerful computer housed in the
part of a package deal a single academic license of lab) and running the program from it. The number
CLC Genomics Workbench and a genome finishing of people that can log on depends on the number of
plug-in (more on plug-ins later). Enrollment in the floating licenses that were purchased. Network/
maintenance, upgrade and support program for the floating licenses are more expensive (typically twice
first 12 months, which was mandatory, was an add- the price) than their single-computer counterparts,
itional $1500, making the initial cost of the software but they can be more economical for big labs or
$7500. Renewal of the maintenance program was classroom settings, where purchasing multiple
25% of the purchase price per year, and, most im- single-user licenses makes less sense. Floating licenses
portantly, was automatic, ‘unless terminated in writ- can also be convenient for groups that have a high
ing by one of the involved parties (CLC bio or the turnover—such as those with a lot of summer stu-
customer) not later than 3 months before the begin- dents and undergraduate volunteers—as they allow
ning of the next calendar year’. In other words, software key codes to be issued to individual lab
9 months after buying the software, I was sent an members and then taken back once the member
invoice for $1500, with 2% interest per month. leaves. Sequencher (Table 1) offers a ‘hardkey’
Although costly, subscribing to the maintenance option, whereby the user is sent a USB dongle
agreement can be wise. Commercial bioinformatics after purchasing the software. Sequencher can then
programs (Table 1), such as Geneious, CLC be loaded onto as many computers as the owner
Genomics Workbench and Lasergene, frequently wants—all that is required to activate the software
undergo major changes, which can significantly im- is plugging in the USB key. But, as I can attest, USB
prove the software. In the past, I have regretted not dongles are easy to misplace (and, if issued from
renewing certain software, and more than once Sequencher, expensive and inconvenient to replace).
I have bought programs anew at full price because Cloud computing has also arrived to bioinfor-
I let the maintenance period expire. matics [20]. Companies like DNAnexus,
Before investing in a bioinformatics package, there InterpretOmics, and others are selling bioinformatics
are other important details to consider. I suggest as a service, whereby consumers buy online access to
asking about the rules on moving the software to powerful computers and their associated software
another computer, in case, for example, you buy a tools, analysis pipelines and data storage and sharing
new laptop or your old one breaks down. I have capabilities. The sequencing giant Illumina sells
found that most companies allow users to transfer online access to their genomics cloud-computing in-
their software license to a different computer. But frastructure BaseSpace—10 terabytes of storage will
doing so normally requires contacting user support run you $12 000 per year. Alternatively, the popular
for a new software activation key, and if you have let web-based platform Galaxy is a free, open-source,
your maintenance agreement expire, then you might cloud-based bioinformatics tool. It is safe to assume
have to renew it before being able to migrate the that bioinformatics clouds will only grow larger and
software. Similarly, if you update your computer more popular over the next few years and are where
operating system—from Apple OS X 10.8 to 10.9, the most innovative new software will be based.
704 Smith

Figure 1: The tools and features commonly found in commercial bioinformatics software packages, and what to
keep in mind when purchasing one.

But what does the software actually do? interphase’. These kinds of claims are often associated
You have paid your money and decided on the best with a white paper describing the software’s de novo
maintenance and licensing options for your needs, assembler, including its algorithm, speed and accur-
now what? Well, it is time to start examining mo- acy, how well it performs on standard datasets, such
lecular sequence data and making some big discov- as the human genome, and how it stacks up against
eries, of course. Commercial bioinformatics packages other brand-name and open-source assemblers.
bring together, into a single browser-based platform, White papers, however, do tend to present commer-
a diversity of nucleotide and protein analysis tools cial software in an overly positive light and—unlike
(Figure 1). These tools do everything from simple open-source programs—only a few of the widely
pairwise alignments to restriction site and gene pre- used proprietary tools have undergone peer review.
dictions to whole genome and transcriptome assem- Commercial browser-based assemblers once had a
blies. Given the prevalence of high-throughput reputation for being slow, memory-expensive and
sequencing in life science research, many of the inferior to the free open-source alternatives. Early
tools are designed for analysing, visualizing and on, I admittedly struggled to generate quality assem-
arranging NGS information. blies, even of small genomes, using commercial
One of the most sought after and marketed fea- programs. In recent years, however, proprietary as-
tures of commercial bioinformatics software is their sembly algorithms have improved immensely and are
ability to perform fast, efficient and high-quality de now used by some of the top academic and industrial
novo assemblies of NGS data—taking millions, even research laboratories in the world. With software like
billions, of single or paired-end sequencing reads and CLC Genomics Workbench v7, I have been able to
assembling them into contigs. Go to any of the big assemble draft genome and transcriptome sequences
bioinformatics software websites and you will find of microalgae from my laptop computer, which has
statements like ‘Dominating the high-throughput 16 GB of memory and an Intel Core i7 processor.
sequencing data analysis challenge’, ‘Quick and ac- Many teams are using proprietary tools to assemble
curate de novo assembly on a desktop computer’ and complex eukaryotic nuclear genomes, including
‘Next-gen sequence assembly with a clear graphical those of land plants. But these kinds of assemblies
 Buying in to bioinformatics 705

require large amounts of time, resources and com- citations for commercial software suites, especially
puting power. their assembly and mapping algorithms, are on the
Commercial assemblers, unlike certain open- rise and catching up to their open-source counter-
source ones, are also great at handling data from dif- parts. A keyword search of ‘CLC Genomics’ in
ferent sequencing platforms, such as assembling a Google Scholar returns >2000 hits. Visit the
mixture of Illumina, 454, PacBio and Sanger reads Geneious blog (http://blog.geneious.com) and you
(Table 1); in fact, for many researchers, this is a will find a section called ‘Citation Sunday’, high-
key selling point. In March 2014, for example, lighting peer-reviewed research that used
Northwestern University purchased an organiza- Geneious. Click the ‘publications’ link on the
tion-wide license of Lasergene, providing all faculty, DNASTAR homepage (www.dnastar.com) and
staff and students with access to the software [21]. you will see a long list of papers and the following
Similarly, the J. Craig Venter Institute has been using bold statement: ‘Every year for the last 28 years,
‘CLC bio’s enterprise platform since 2009 and more researchers have cited DNASTAR’s software
currently uses it on more than 30 research grants, in scientific journals than any other sequence analysis soft-
including their work as part of the Human ware’ (italics their own). Skimming through these
Microbiome Project’ [22]. publications, it is obvious that most papers citing
Read mapping, which is when sequencing reads proprietary programs reference a range of open-
are aligned to a reference, such as an entire chromo- source ones as well, and that contemporary genomics
some or genome, is another core feature of commer- research often involves a hodgepodge of commercial
cial bioinformatics packages. Like with the de novo and free bioinformatics software. Lizzy Sollars, a PhD
assemblers, bioinformatics companies regularly student at CLC bio, put it best when describing her
boast about their highly tuned, ultra-fast mapping work on the Ash Tree Genome Project: ‘Using CLC
algorithms for reference-guided alignments. CLC bio’s de novo assembler, along with the open-source
bio maintains that their ‘read mapper not only scaffolding tool SSPACE, we produced our best de
maps more than 1.3 billion Illumina reads (100 nt, novo assembly so far’ [26]. Visit the Broad Institute
paired-end) in less than 5 hours, but [that it] also Software Archive (www.broadinstitute.org/scien-
achieves consistently high mapping accuracy even tific-community/software) for a list of widely used
for complex read data, such [as those] originating open-source tools for analysing large genome-related
from the PacBioRS system’ [23]. They go on to datasets.
argue that the CLC ‘mapper consistently outper-
forms the market in all major disciplines’, including More than just browser-based assemblers
the open-source peer-reviewed mapping algorithms and mappers
Bowtie 2 and BWA [23]. Geneious makes similar Commercial sequence analysis suites, in addition to
claims about their proprietary mapper: ‘Six read assembling and mapping NGS data, are designed to
mapping algorithms were evaluated on Illumina carry out the day-to-day bioinformatics tasks
HiSeq and Ion Torrent sequence data from an involved in molecular, evolutionary and genome
Escherichia coli—BWA (0.6.2-r126), Bowtie 1 biology (Figure 1). Although it might sound trivial,
(0.12.8), Bowtie 2 (2.0.0-beta7), SMALT (0.6.4), one of the more useful features of commercial pack-
SOAP2 (2.20) and Geneious (6.0.3). The results ages is visualizing, organizing and storing molecular
demonstrate that the Geneious Read Mapper pro- sequence information. The intuitive graphical inter-
duces superior results to the other mapping algo- faces of commercial software allow users to easily
rithms on these data sets’ [24]. The claims can be build folder hierarchies and drop-down lists of se-
overstated, but in my experience commercial read quence data, move or export these data to different
mappers are as good as or outperform many of the folders and change file formats for use in other ap-
open-source alternatives. plications. In most cases, the software can connect to
The ultimate test for any assembler or read mapper online resources, such as the National Centre for
is whether it is cited in peer-reviewed journals. Biotechnology Information (NCBI) and UniProt,
There is no question that open-source programs providing quick direct access to vast amounts of nu-
are cited more than proprietary ones. The paper pre- cleotide and protein sequence information, which
senting the mapper Bowtie 2, for instance, has can then be downloaded, interpreted and analysed
received 700 citations in just 2 years [25]. But through interactive sequence viewers. Many
706 Smith

commercial programs also give users the ability to bioinformatics packages is continually expanding.
BLAST [4] their data directly against NCBI and Plug-ins work in two ways: they allow users to
UniProt databases, or custom databases, and view add more features to the software, but they also
and analyse the results through GUIs. My research allow developers to design their own apps for the
on organelle DNA has benefited greatly from these software. Bioinformatics plug-ins can bring some of
types of search tools—in minutes, using commercial the most commonly used open-source software to
software, I can download all of the completely proprietary programs, giving users the benefits of a
sequenced mitochondrial and chloroplast genomes user-friendly GUI and the power of peer-reviewed
from GenBank, extract their annotations, sort and algorithms. A cursory scan through the plug-in list
search them based on a range of features and transfer for Geneious reveals programs for phylogenetics (e.g.
them to subfolders for downstream analyses. GARLI [31], MrBayes [16] and RAxML [32]), NGS
The applications within commercial bioinfor- assembly and mapping (e.g. Velvet [33], TopHat [34]
matics suites that I tend to use most often are for and Bowtie [25]), sequence alignment (e.g. ClustalW
evolutionary analyses and comparative genomics. [13], MAUVE [14] and Muscle [35]) and other
Most packages come with software for aligning molecular analysis procedures (e.g. Glimmer Gene
nucleotide and amino acid sequences (and entire Prediction [36], Phobos Tandem Repeat Finder
chromosomes) as well as tools for inferring evolu- (e.g. [37]) and DualBrothers Recombination
tionary relationships among sequences and con- Detection [38]). More plug-ins means more func-
structing phylogenetic trees and distance matrices. tions and sometimes more money. CLC bio provides
Other useful tools include protein structure predic- a wide range of plug-ins for their Genomics
tion, nucleotide repeat and motif finders and primer Workbench package (www.clcbio.com/clc-plugin),
prediction software. An advantage to performing many of which are free, but some can cost hundreds
these kinds of analyses within commercial software even thousands of dollars—the Shannon Human
is that the results—be they genome maps, align- Splicing Pipeline plug-in is around $4000.
ments, nucleotide sequence dot plots or phylogen- Once you have found the tools and plug-ins to
etic trees—are depicted in colourful and editable suit your needs, you can start linking them together
graphics, which can be exported and used for figures into ‘workflows’ and pipelines. As CLC bio puts it:
in lectures and publications. I regularly build genome ‘A workflow consists of a series of tools where the
maps with Geneious and then export them to a output of one tool is connected as the input to an-
graphics-editing program for further polishing. All other tool. This way you can set up a workflow to
of the genome maps in Smith et al. [27, 28], for ex- go through (for example) read mapping, using the
ample, were constructed with Geneious. The inter- mapped reads as input for variant detection, and per-
active graphical visualization tools of commercial form filtering of the variant track’. Workflows
suites are excellent for exploring large genomic can save researchers huge amounts of time and are
data sets (often depicted in stacked views) and becoming more widespread among commercial bio-
allow for quick navigation to regions or contigs informatics packages. If you do not want to fork
of interest. Many of these features parallel those of out the big bucks, check out The Galaxy Project
popular freely available NGS viewers, like the (http://galaxyproject.org)—a free, web-based and
Interactive Genomics Viewer [29] and Tablet [30]. user-friendly bioinformatics workflow management
If you purchase a bioinformatics package and dis- system, which provides access to a large number of
cover that a particular function is missing, do not data integration and analysis programs.
panic because there is probably a ‘plug-in’ that can
do the job. Plug-ins are downloadable applications Bringing bioinformatics into the
that provide additional features to software pack- classroom
ages—similar to apps for smartphones and tablets. Students today are reared on a digital diet of smart-
For bioinformatics software, plug-ins add an array phones, tablets and ultra-sleek retina-display laptops
of new sequence analysis tools (ones that comple- filled with intuitive software apps, which integrate
ment existing tools or that add novel functions), seamlessly across platforms and devices. Thus, when
greatly improving the package. Companies are con- these students are introduced to bioinformatics and
stantly designing new plug-ins for their software, molecular evolution, one would expect them to
which means that the repertoire of tools within engage more easily and enthusiastically with
 Buying in to bioinformatics 707

easy-to-use GUI software than with barebones com- certain operations are turned off (e.g. assemblies
mand-line-driven tools. cannot be exported or saved). However, even with
Commercial bioinformatics suites, given their limited functions, the software can still provide
browser-based point-and-click interface, lend them- enough processes for teaching and developing assign-
selves to teaching and learning. From a lecturer’s ments [39]. Again, there is nothing preventing in-
perspective, the high-end graphics, visual aids and structors from investing in a personal copy of the
tutorials built into proprietary software are great for software and using it for lectures.
communicating bioinformatics topics, themes and
procedures, from sequence alignments to contig Give it try and give us your feedback
assemblies to blasting proteins against GenBank. Going forward, innovations in molecular sequencing
I regularly incorporate bioinformatics software techniques will result in ever more sophisticated bio-
suites into my undergraduate lectures and conference informatics programs, and it is crucial that these pro-
presentations. With my notebook computer con- grams are accessible to a broad range of users. We
nected to a projector, I can use a program like might soon be at a point where walk-in medical
Geneious to effectively communicate to a large audi- clinics have genome sequencing and bioinformatics
ence the procedures and output of various bioinfor- desks, where patients can play an active role in in-
matics analyses. For example, using a bioinformatics terpreting their gene sequences and contributing to
package, it takes me 10 min to import a set of genetic treatments, and where high-school students
Illumina sequencing reads, download a reference assemble and analyse genomes for homework. The
genome from GenBank, map the reads to the refer- increasingly integral role of bioinformatics in re-
ence and then zoom in to the resulting alignment, search, medicine and society also means that it will
showing the class where the reads mapped onto the become an increasingly larger, more lucrative indus-
genome, the polymorphic sites, paired-end distances try and one where users will have to pay for the best
and an assortment of other statistics. With the same products.
software, I can design, distribute and evaluate bio- My own experiences with proprietary bioinfor-
informatics assignments to be completed inside or matics software have been positive. The tools I
outside of the classroom. These assignments typically have purchased have made my laboratory group
involve a range of sequence analysis tools where the and me more productive, and I certainly enjoy
results of one tool are used as input for another. using stand-alone GUI-based programs more than
I almost always receive positive feedback from command-line driven ones. This productivity and
students when using user-friendly bioinformatics— ease of use, however, has come at a cost, both intel-
some students have even said that it has inspired lectually and financially. Although I use sequence
them to pursue a career in bioinformatics. analysis tools almost every day, my bioinformatics
Obviously, the biggest barrier to bringing com- skills, in certain respects, have plateaued. Moreover,
mercial software into the classroom is the high finan- the licensing and upgrading costs of using commer-
cial cost of the programs. It is unreasonable to ask cial software represent a significant proportion of my
students to pay hundreds of dollars for proprietary laboratory’s operating budget. Another downside to
software, and most undergraduate departments are commercial bioinformatics is that the user can lose
unable or unwilling to invest thousands of dollars touch with what the programs/algorithms are actu-
into bioinformatics teaching resources—although ally doing (they can be a ‘black box’), whereas it is
with institutes like Northwestern buying campus- simple to look ‘under the hood’ of open-source
wide access to proprietary programs, this might be tools, which makes them easy to modify and de-
changing. velop. But as bioinformatics software and algorithms
One strategy for using commercial bioinformatics become increasingly complex, it might be unrealistic
in a course is to get all of the students to apply for a to expect students to have a strong grasp of the math,
free trial version of the software. Their access to the theory and computer science that underpin those
software will be limited to 30 days, but this should processes.
be long enough for them to complete a few assign- If you are considering commercial programs, I
ments or workshops. Alternatively, some commercial recommend taking advantage of the free trials that
bioinformatics packages can be downloaded and used most of the bioinformatics companies offer. You
for free on a ‘basic’ or ‘test’ mode, which means that may find that these programs streamline your
708 Smith

research and invigorate your classroom, or that they 8. Tamura K, Stecher G, Peterson D, etal. MEGA6: Molecular
Evolutionary Genetics Analysis version 6.0. Mol Biol Evol
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Wherever you stand on the topic, I urge you to share UGENE: a unified bioinformatics toolkit. Bioinformatics
your opinions and experiences with others—and best 2012;28:1166–7.
of luck with all of your bioinformatics endeavours. 10. Vincent AT, Charette SJ. Freedom in bioinformatics. Front
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13. Larkin MA, Blackshields G, Brown NP, et al. Clustal W and
 Often marketed as one-stop bioinformatics toolkits, these soft-
Clustal X version 2.0. Bioinformatics 2007;23:2947–8.
ware packages can be expensive, and it can be difficult for con-
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 This review explores some of the currently available proprietary alignment of conserved genomic sequence with rearrange-
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 Some commercial bioinformatics programs are arguably over- lihood. Mol Biol Evol 2007;24:1586–91.
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The author thanks four anonymous reviewers whose feedback
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University adopts DNASTAR Lasergene software. http://
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