Geneious Bioinformatics Software Review

The science of today is the technology of tomorrow! And we believe that tomorrow has arrived now! With the establishment of a separate course named Bioinformatics, we have entered into a new era of learning.

Hello fellow scientists! Are you stuck in one of your Biosciences projects that requires substantial computational analysis? Or are you on the verge of breakthrough discovery? Is the thought of choosing the right Bioinformatics software haunting you? Then you have arrived at the right piece of writing.

In this review article, I bring you a review of Geneious, a widely known Bioinformatics software. This Geneious review shall cover all the aspects of this software like what the tool is all about. Why should it be used and why it shouldn’t? Is it cost-effective or not, and my final thoughts about it?

Keep reading on until you find all the answers to your biological puzzle.

Geneious: What this Software is all about?

Geneious software is a biological analysis software created in Java Swing. The rate of interoperability is significantly high due to this among all commonly used Operating systems.

The Geneious software allows extensive visualization, manipulation, and transfer of DNA of all types like circular, straight, oligos, etc. along with peptide chains, multiple alignments, phylogenetic trees, contig assemblies, statistical graphs, 3D structures, chromatograms, electropherograms.

The list is endless. If you wish to know the countless features, keep reading the upcoming sections.

 

9 Key Features of Geneious- What does it offer?

Geneious is a platform for the scientific amalgamation of molecular biology, genetics, and computational applications. It performs tasks of analysis via a simple user interface. Some of the highlighted key features include:

[1] Next-Generation Sequencing Assembly and Analysis 

One of the most important molecular analyses is NGS technology. With the help of the Geneious tool, data can be imported in a wide range of formats. After data import, the pre-processing takes place.

The reference mapping and de novo assembly are flexible. Bowtie and Velvet options are available on the Geneious Server for analysis of NGS data.

[2] Visualizations and Graphics 

The 3 3-dimensional structures can be visualized briefly with proper labels. The sequence, alignments, assemblies, annotations, and restriction sites can be visualized.

The secondary structure of RNA can be visualized too. The construction of phylogenetic trees, dot plots, and virtual gels is possible via Geneious software.

[3] Editing and Assembly of Chromatogram 

The Sanger sequencing data is assembled on the chromatogram. The Sequencher data is imported from .CAF file. The assembly of sequences takes place in order of their name. It is also possible to call the secondary peaks on this tool.

[4] Alignment and Phylogenetics 

The sequence alignment features are exhibited by this software. All the major alignment algorithms such as MUSCLE, MAFFT, MAUVE genome, translation, and profile alignments can be executed. ClustalW which is also a type of alignment algorithm is embedded to it.

The phylogenetic involves the study of evolutionary relationships. Trees such as Neighbourhood Joining (NJ), UPGMA, PhyML, etc can be constructed. Bootstrapping and consensus tree development choices are also provided. The tree viewing is in interactive mode.

[5] Cloning 

It is a one-step process for multi-site Gateway cloning. One step for inserting the fragment of DNA into the vector. The virtual gel viewer is enabled for viewing the process. The restriction digestion is executed too. It shows the non-cutting enzymes.

[6] Database Exploration 

The biological databases available on different platforms can be retrieved on Geneious. The literature search, sequence search, local search, and automated searching agents can be employed on the software. General BLAST and custom BLAST searches such as protein-protein BLAST, DNA-DNA BLAST, protein-DNA BLAST, etc. can be executed too.

[7] Primer Design 

The PCR primers and probes for the process of amplification can be designed here. The software has an in-built PCR primer database. You can choose the primer as per your requirement by testing the Primer to the sequence. However, the sequencing and multiplex primers are yet to be launched on the platform.

[8] Prediction and Manipulation 

The secondary structures of protein can be predicted. Sequences such as ORFs repeats, and CpG islands can be known. Besides these, the cleavage sites and transcription factors can be identified. The Antigenic regions, Pfam domains of the protein structure, SNPs, INDELS, and coverage can be interpreted and annotated.

[9] Biocode LIMS

It manages the sequences in 96/384 well plates. It can import the chromatograms and attach them to the well plates. The bin and trim of chromatograms if followed after the attachment process. The Taxonomy and Genbank can be verified. It allows Genbank submission as well.

 

Performance Analysis

The parameter to define the goodness of any software is the quality of output. Here we have a short yet appropriate description of one of the mapping tools.

The figure given below is the de novo assembly of the raw Oxford Nanopore and PacBio long-read sequences. Using the plugin Flye both genome projects and metagenome assembly can be performed.

Here the Reference sequence is E.coli K12 MG1655 along the Mapper Minimap2. The data type is sensitive that is less than a 5% divergence in results which is actually good.

Some significant papers with Geneious citations that recently got published are:

• Chong, Yoong Min, et al. “Complete Genome Sequences of SARS-CoV-2 Strains Detected in Malaysia.” Microbiology Resource Announcements, vol. 9, no. 20, 2020.
• Deng, Xianding, et al. “Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California.” Science, June 2020
• Jaimes, Javier A., et al. “Phylogenetic Analysis and Structural Modeling of SARS-CoV-2 Spike Protein Reveals an Evolutionary Distinct and Proteolytically Sensitive Activation Loop.” Journal of Molecular Biology, vol. 432, no. 10, May 2020, pp. 3309–25
• Stefanelli, Paola, et al. “Whole genome and phylogenetic analysis of two SARS-CoV-2 strains isolated in Italy in January and February 2020: additional clues on multiple introductions and further circulation in Europe.” Eurosurveillance, vol. 25, no. 13, Apr. 2020, p. 2000305
• Zehender, Gianguglielmo, et al. “Genomic characterization and phylogenetic analysis of SARS-COV-2 in Italy.” Journal of Medical Virology, vol. n/a, no. n/a, Mar. 2020

Some significant papers on RNAseq published with the help of the Geneious tool are:

• Hidalgo-Cantabrana, Claudio, et al. “Genome editing using the endogenous type I CRISPR-Cas system in Lactobacillus crispatus.” Proceedings of the National Academy of Sciences, vol. 116, no. 32, Aug. 2019, p. 15774
• Brettell, Laura E., et al. “RNAseq Analysis Reveals Virus Diversity within Hawaiian Apiary Insect Communities.” Viruses, vol. 11, no. 5, May 2019, p. 397
• Alcolea, Pedro J., et al. “RNA-seq analysis reveals differences in transcript abundance between cultured and sand fly-derived Leishmania infantum promastigotes.” Parasitology International, vol. 67, no. 4, Aug. 2018, pp. 476–80

You must read these articles to know the participation of the tool in developing significant results.

 

Pricing Packages

Geneious offers two powerful platforms for modern life sciences research—Geneious Prime for molecular biology and sequence analysis, and Geneious Biologics for antibody discovery and biologics research. Below is a detailed breakdown of their pricing structures and what each plan provides.

Geneious Prime Pricing

Geneious Prime is designed to serve the needs of individual researchers, academic groups, and commercial organizations by providing advanced tools for sequence analysis, cloning, alignment, and more. The platform is available through two main subscription models: Team Subscriptions and Personal Subscriptions—with a special offering for course licenses.

Team Subscriptions

Tailored for groups and organizations, these plans include secure cloud-based storage, collaboration tools, and streamlined user management:

• Academic Team Subscription:
  • 2 Users – $1,280/year: Ideal for small academic or research groups, offering essential collaborative tools and data management.
  • 5 Users – $3,200/year: Expands the collaborative capabilities for mid-sized teams with additional user seats.
  • 10 Users – $6,400/year: Provides extensive access for larger academic or non-profit groups, ensuring all team members can work together seamlessly.
• Corporate Team Subscription:
  • 2 Users – $4,500/year: Designed for commercial organizations, this plan ensures secure and efficient collaboration for small corporate teams.
  • 5 Users – $11,250/year: Supports mid-sized corporate teams with enhanced collaborative features and data management.
  • 10 Users – $22,500/year: Best suited for larger commercial teams that require robust collaboration and centralized license administration.
• Enterprise Team Subscription:
  • Custom Pricing: For organizations with advanced needs, the enterprise option includes features such as single sign-on (SSO), SCIM integration, audit tracking, expanded cloud storage, and a public REST API—allowing complete customization of the collaborative experience.

Personal Subscriptions

For individual researchers who prefer a solo license, Geneious Prime offers plans that cater to different user types:

• Student – $200/year: Specially priced for students in active degree programs, this plan provides full access to the suite of molecular biology tools at a budget-friendly rate.
• Academic – $595/year: Designed for individuals in academic or government organizations, this plan delivers comprehensive features along with regular updates and dedicated technical support.
• Corporate – $1,950/year: Aimed at professionals in commercial settings, this subscription offers all the essential features of Geneious Prime along with premium support and cloud connectivity.

Course Licenses

• Free for Educators: Professors and teachers can provide Geneious Prime access to their students as part of a course at no additional cost, enabling a hands-on learning experience with cutting-edge molecular biology software.

They also offer a trial, you can go for the free trial version of 14 days before subscribing to any of the packages. See if it meets the needs of your labs and research. If it does, give it another serious thought and then buy.

Geneious Biologics Pricing

Geneious Biologics is a dedicated platform for antibody discovery and biologics research. It offers flexible subscription options—from a free starter plan to premium and group plans—designed to scale with the needs of individual researchers and collaborative teams.

• Starter Plan – Free: This entry-level plan is perfect for individual users looking to get a taste of the platform’s capabilities. It includes:
  • Single-user access for antibody annotation focused on IgG-like molecules.
  • Analysis of up to 24 sequences.
  • Interactive sequence visualizations and a 7-day window to access the results.
  • A great way to explore the core functionality of antibody discovery without any upfront cost.
• Personal Plan: A premium solution for individuals requiring more advanced antibody screening, analysis, and visualization:
  • Corporate – $9,500/year: Tailored for professionals in the commercial sector, this plan includes enhanced analysis tools, support for multiple antibody types (such as Fab, VHH, scFv, and TCR), and advanced statistical features.
  • Academic – $4,750/year: Offered at a discounted rate for academic users, this plan provides the same premium features to support high-throughput antibody discovery and detailed sequence analysis.
• Group Plan: Designed for teams that need to share data and collaborate on antibody discovery projects, the Group Plan builds on the Personal Plan features by adding:
  • Collaborative tools for result sharing.
  • Advanced user administration to manage multiple team members.
  • Custom Pricing: Contact Geneious for a quote tailored to your team’s size and specific research requirements.
• Short Term Project Option: For those with temporary needs, Geneious Biologics offers a 3‑month personal license:
  • Corporate – $4,500 per quarter.
  • Academic – $2,250 per quarter. This option is ideal for short-term projects or pilot studies where flexibility is key.
• Free Trial: Interested users can request a 30‑day free trial of the premium version of Geneious Biologics to evaluate its full feature set before making a commitment.

 

Pros and Cons of Geneious Bioinformatics Software

The Pros

Geneious can be considered as a prima facie tool for initial studies of an unknown sequence. Some advantages that make it unique are mentioned below:

• A good choice to carry out the Sequence Analysis and Genomics study.
• User-friendly with an intuitive interface
• Essential genomic tools are embedded for NGS, Sanger, and long-read sequence analysis
• Allows multiple and pairwise alignments, de novo assembly, mapping, visualization, annotation, prediction, and phylogenetic analysis
• It can perform primer designing and cloning operations
• Annotation of plasmid maps and vectors
• Finds CRISPR sites and codon optimization
• Management of data
• Simple drag-and-drop options
• Import and export and conversion of sequences and annotations
• Supported by Mac, Windows, and Linux platforms
• Additional benefits: Automatic workflows, Avail the Geneious Server database for data security, add plugins to increase the functionality

The Cons

Geneious has thousands of citations yet it has some drawbacks that you must consider before jumping to any conclusions. These disadvantages are mentioned below:

• Yes, the price can be a bit too much for what it provides
• Upgradation can cost more money in the subsequent years of subscription
• The time duration for obtaining analysis outputs can be longer

 

User Experience

Most of the Bioinformatical tools are often complained about for the difficult user interface. However, the case may be different in some software like Geneious which uses a click interface instead of a command-line.

Geneious is certainly designed for easy usage. Single-button clicks make it much more intriguing. The software is user-friendly, without a speck of doubt. However, the time taken to generate results for the analysis might be longer than usual due to congestion.

The step-wise tutorials and guide make the process of data retrieval, processing, and analysis easy peasy for the users. The guide videos for beginners are also provided. The Customer support seems promising. The next section includes how the Customer Support system of Geneious works.

 

Customer Support

I think the user-friendliness comes from the excellent Customer Support system. It feels like there is nothing to worry about once you start exploiting the tools.

There is a whole load of tutorials with data for step-wise understanding. There is a user manual that guides through every inch of the application. The videos and handbooks for understanding the software are mesmerizing.

There is a community of users who can take questions from other users. It is also called as Plugin Development Forum. Contact support is provided via email. You can directly contact the developers for any queries and assistance.

 

Limitations of The Software

Geneious is truly a genius in its own way. It has settled most of our problems by providing all analysis quests at a single platform. However, some of the limitations that have come into the picture include the following:

• Some users are struggling with a trial version. All the analysis options are not live in the free trial version.
• Some face issues while designing the primer. There are limitations
• People use BioEdit software, a free and easy-to-use sequence analysis application to overcome these limitations
• For general alignment, BLAST is the best choice

Check Our List of Top 30 Best Bioinformatics Software & Tools [Free + Paid]

Final Thoughts!

This article contains an articulate analysis of the Bioinformatical software Geneious. The aspects of Features, Pros & Cons, Price, User support etc. was covered briefly. The functionality and major domains of scientific fields have been discussed too. In conclusion, I would like to summarize the article with some key points:

• Software is online
• Easily available
• User-friendly
• Easy-to-understand interface
• Cost-effective
• Accurate results
• Clear visualization
• Statistical graphs
• Fast and precise NGS workflow
• PCR and probe design
• Phylogenetic analysis
• Database search
• Price can be burdening
• The time for calculations might be longer
• Data can be stored on a server but security remains a big question
• An extra charge for version upgradation might be asked for

Considering all the above points, I would recommend you try this tool at least once. You can undergo a trial period of 14 days. Go ahead only when you find it reasonable and worth the price.

It happens very rarely that a platform comes with so many integrated tools with the choice to add more plugins for additional functionalities. But it is also unavoidable that it comes with some drawbacks too.

You may want to read our articles on DNASTAR Lasergene, SeqBuilder Pro, CLC Main Workbench, Sequencher to find the most appropriate tool for your set of data.

Given below are the FAQs that relate to the Geneious software. Go through them once in case you have doubts.

Frequently Asked Questions

How do I renew my existing subscription?

1. Select your plan of choice
2. Enter the previous license key
3. Fill payment information
4. Subscription is renewed

What is the difference between a personal and a group plan?

A group plan is for the team. The number of seats is equal to the number of machines which install the software.

A personal plan is for one person only. The software can be downloaded on two devices but only one device runs the software at a time.

How do I buy a student plan?

By availing of the Geneious Prime student subscription, not through Purchase Order

Am I eligible for student pricing?

Only individuals enrolled for undergraduate and postgraduate courses can apply for this plan. A student license is allocated to student buyers.

What happens when my subscription expires?

The Geneious Prime subscription reverts to restricted mode on expiration. Most of the functions are disabled, though file import export is allowed. Data can be visualized too.

What support is offered?

Multiple tutorials and resources for step-by-step learning are available. On availing of the Geneious Prime subscription, access to the scientific support team is also granted.