Comprehensive sequence analysis software for sequence alignments, Sanger sequencing, virtual cloning, primer design, plasmid maps, sequencing editing, and more.

Every molecular biologist needs reliable sequence analysis software for everyday tasks such as editing and aligning sequences and designing workable primers and clones. And while these tasks may be routine, their success impacts everything else downstream. That’s why it’s so important to have dependable, easy-to-use tools that get it right, every time.

Lasergene Molecular Biology has you covered for important sequence analysis tasks including multiple sequence alignments, PCR primer design, in silico cloning, and Sanger sequence assembly. Now you can reach your analysis goals more quickly with insightful features like batch editing, automated sequence annotation, access to a meticulously annotated plasmid vector map catalog, and full integration with NCBI databases. Lasergene Molecular Biology goes beyond the basics, delivering truly remarkable sequence analysis software that you can rely on.

Lasergene Molecular Biology Workflows

Automated Virtual Cloning

Use SeqBuilder Pro to be confident in your cloning experiment in the lab, every time!

At its core, the process of molecular cloning is quite simple, but without proper planning and preparation, even the simplest cloning experiment will go wrong quickly. Virtual cloning using SeqBuilder Pro enables you to easily and confidently plan your cloning experiment so that you get it right in the lab. SeqBuilder Pro offers unmatched flexibility to help you meet your experiment requirements, including the ability to batch clone groups of fragments simultaneously, and guides you step-by-step in preparing your vectors and amplifying your inserts using all of the most popular cloning methods: Gateway, Gateway Multisite, Gibson, GeneArt, In-Fusion, TA, TOPO, and PCR-directed restriction enzyme cloning. In silico cloning in SeqBuilder Pro gives you the proper planning and preparation you need to be confident in your cloning experiments, every time!

Clone Sequence Verification

Use SeqBuilder Pro to confirm the accuracy of your clone created in the lab.

You’ve finished creating your clone in the lab and are ready to move on to downstream experiments, but how do you know that all your steps have resulted in the expected recombinant clones? Many researchers verify their clone accuracy through Sanger sequencing. We make it easy to perform clone sequence verification to confirm that your Sanger sequencing results perfectly match the clone you designed. Our clone sequence verification workflow confirms that the clone fully contains the insert of interest in the correct orientation, is in-frame with the vector, and confirms that there is adequate coverage of trace files across the entire clone. If discrepancies are identified during the clone sequence verification process, we show you exactly where the disagreements lie, so that you can address them. Use SeqBuilder Pro’s clone sequence verification workflow to catch read misalignment and insertion errors before proceeding with downstream experiments.

Gel Electrophoresis Simulation

Skip the trial and error and confirm your ideal conditions using gel electrophoresis simulation in SeqBuilder Pro!

Gel electrophoresis sometimes takes a lot of prep work and trial and error to determine the perfect percent agarose and set of molecular weight markers to resolve your DNA fragments. Other times, restriction digests produce such complicated restriction patterns that it can be difficult to determine if the restriction digest was complete. That’s why we offer virtual gel electrophoresis in SeqBuilder Pro, which allows you to apply different restriction enzymes to one or more DNA fragments and simulate digests to determine the expected size of products on an electrophoresis gel. Use gel electrophoresis simulation to easily determine the ideal percent agarose and set of molecular weight markers to resolve your DNA fragments before running gel electrophoresis in the lab. Once you run the actual gel in your laboratory, you can place the gel or its image side-by-side with the virtual gel electrophoresis image to confirm gels that have complex banding patterns. Skip the trial and error and confirm your ideal conditions using gel electrophoresis simulation in SeqBuilder Pro!

Mauve Genome Alignment

Use MegAlign Pro to easily perform a Mauve genome alignment and compare multiple genomes with structural complexity.

In the realm of multiple sequence aligners, the trusted Mauve algorithm stands apart from its traditional counterparts through its ability to align chromosome length sequences and sequences that contain structural rearrangements. Multiple genome alignments often require methods separate from traditional multiple sequence aligners, requiring you to go between various tools for your analysis. That’s why we’ve seamlessly integrated the Mauve algorithm into MegAlign Pro, so that everything you need for all of your multiple sequence alignments is in one easy-to-use application. Simply drag and drop your genomes into MegAlign Pro and perform a Mauve genome alignment using the default settings, or modify parameters to meet your needs. Following the genome alignment, MegAlign Pro makes it easy to navigate to and view conserved regions across multiple sequences, even at various zoom levels. Customize the appearance of your alignment as desired before exporting a publication-quality, editable image. Use MegAlign Pro to easily perform Mauve genome alignments in the same application you trust for all your multiple sequence alignment needs.

Multiple Sequence Alignment

Use MegAlign Pro for accurate sequence alignment and in-depth analysis.

It’s no secret that there are many multiple sequence alignment tools out there, but an initial sequence alignment only gets you so far. It’s the post-alignment analysis that really moves you down the path of answering your research questions. MegAlign Pro offers everything you need for each stage of a multiple sequence alignment, not only the algorithms needed for aligning both gene-level and genome-scale sequence data, but also the capability to dig deep in the post-alignment stage.

MegAlign Pro guides you through the post-alignment process, including generating and comparing multiple phylogenetic trees, and identifying and analyzing variants across genomic strains. You can easily separate interesting regions for new subalignments, edit and trim individual sequences or the entire alignment, and customize the appearance of your alignment before generating high-quality images, suitable for publication.

Sequence alignment software features

Align DNA, RNA, or protein sequences using Clustal Omega, Clustal W, MAFFT, MUSCLE, and Mauve multiple sequence alignment methods.
Utilize automated guidance to choose an alignment method for your specific sequences based on quantity, length, and type.
Identify and evaluate variants between viral, mitochondrial, or chloroplast genomes.
Easily trim ends at the beginning or end of an alignment.
Realign a range of aligned sequences using different parameters or a different alignment method.
Create profile alignments by merging two existing completed alignments together.
Generate, customize, and compare multiple phylogenetic trees using RAxML, for computer Maximum Likelihood trees, or the Neighbor Joining method.

Pairwise Sequence Alignment

Use MegAlign Pro to easily perform multiple and pairwise sequence alignments.

Sometimes, examining a pair of sequences from a multiple sequence alignment directly may give you a better picture of the relatedness of the pair. Additionally, sometimes pairwise sequence alignment is simply more suitable than multiple alignment, for example, to align the sequence of an uncharacterized gene to the genome of a related reference strain. MegAlign Pro gives you the flexibility to perform local, global and semi-global pairwise sequence alignments using the industry standard Smith-Waterman and Needleman-Wunsch algorithms, all within the same application you use for multiple sequence alignments and post-alignment analysis. This makes it easy to further explore the relatedness of pairs of sequences from multiple alignments, align transcripts to genes, or find a gene within a genome.

PCR Site-Directed Mutagenesis

See the structural impact of a mutation before designing your primers.

PCR site-directed mutagenesis is one of the most often-used techniques for introducing a mutation into a DNA sequence, however most software tools don’t consider the impact of a mutation on protein structure when designing primers. Lasergene provides a unique approach to primer design for PCR site-directed mutagenesis by first focusing on predicting which mutations introduced into a DNA sequence may lead to changes in protein stability. Using our hot spot scanning and create variant tools, you can quickly see what mutations will increase or decrease fold stability. Once optimal candidate variants for your experiment are determined, you are ready to create PCR primers to introduce them into your sequence using our point-and-click tools for designing and mutating primers. The unique combination of our structure modeling and primer design tools saves you time and money compared to traditional trial-and-error approaches to mutagenesis experiments.

PCR Primer Design

Use SeqBuilder Pro to design PCR primers you can rely on to work the first time.

Let’s be honest, there is nothing more discouraging than spending the time and money setting up a PCR reaction only to have it fail multiple times. Though many factors can impact the success of PCR, often when failure happens, poor PCR primer design is the culprit. SeqBuilder Pro eliminates this problem by designing PCR primers matching your unique experimental conditions and giving you the ability to see the impact of potential changes before you try them out in the lab. A perfect balance of guidance, editability, and customization, SeqBuilder Pro enables you to design PCR primers that you can rely on to work the first time.

Phylogenetic Analysis

Accurate and thorough phylogenetic analysis software

Phylogenetic analysis is a fundamental facet of molecular biology, and our primary tool for understanding evolutionary relationships between genes, organisms, and populations. MegAlign Pro offers a comprehensive, easy-to-use interface for integrated multiple sequence alignment and phylogenetic analysis – no clunky plugins required. Effortlessly build phylogenetic trees using neighbor-joining or Maximum Likelihood (RAxML) analysis options, generate multiple trees for side-by-side comparisons, generate bootstrap support values, and more. Customize the appearance of your phylogenetic tree before exporting as an image for publication or collaboration.

Plasmid Map Creation

Rely on SeqBuilder Pro for beautiful, accurately annotated plasmid maps!

Whether you are creating a plasmid map for publication, or to use in a cloning experiment, having a clearly annotated plasmid is essential. Many plasmid design tools lack formatting options and are cumbersome to use, resulting in hard to read maps that are often missing features and restriction sites critical to your experiment. SeqBuilder Pro plasmid map software offers an elegant interface that makes it easy to create and annotate graphically rich maps for cloning, collaboration, and publication. Effortlessly display and customize sites and features, and take advantage of our built-in automated tool to accurately annotate your plasmid using our extensive, curated database of features. SeqBuilder Pro also includes a custom vector catalog, which offers meticulously annotated plasmid vector maps for use in in silico cloning. Say goodbye to clumsy tools and rely on SeqBuilder Pro to easily create and customize beautiful plasmid maps!

Flexible plasmid design software

Import virtually any type of sequence file.
Utilize and customize the curated Feature Library for auto-annotation
Display enzymes based on the frequency of cuts, type or class, site complexity, overhang compatibility, or an intersection of any of these groups.
Click and drag to reposition enzyme labels — other labels move automatically to avoid overlapping
Easily show/hide features and customize feature appearance
Export images for publication or collaboration.

Sanger Sequence Assembly

Be confident in the accuracy of your assembly.

Assembling your sequencing data is one of the most critical steps in DNA sequencing because accuracy is so important. The assembly algorithm we use in our Sanger sequence assembly software has been proven to be the most accurate on the market for Sanger ABI sequencing data. When compared to the competition, our algorithm does the best job assembling sequences into a single contig, and calling the most accurate consensus sequence based on trace quality and shape. Following assembly, SeqMan Ultra uniquely offers you the ability to easily edit your assembled data – exposing or trimming ends, introducing mutations – as well as analyzing your assembled data, including viewing chromatograms, evaluating coverage and analyzing variants. Getting it right matters. Use the sequence assembly tools in SeqMan Ultra and be confident in the accuracy of your assembly.

Sequencing Editing and Annotation

Use SeqBuilder Pro for comprehensive sequence editing and annotation in one easy-to-use application!

Sequence editing is such a primary part of molecular biology research that it may seem like any sequence editing software will do. But ultimately, the convenience and capabilities of the tools you choose do matter. SeqBuilder Pro not only offers all of the expected functionality of a sequence editor: the ability to change nucleotides and amino acids, translate, reverse complement, add features, identify ORFs, and introduce restriction sites, but additionally provides automated batch editing tools so that you can seamlessly create and edit groups of sequences simultaneously, allowing you to accomplish your sequence editing goals faster. The live, interactive views in SeqBuilder Pro make it effortless to edit and annotate your sequences, customize your features and create plasmid maps. Our sequence editing software is also integrated with NCBI databases, making it easy to access and search online databases. The tools you use matter. Use SeqBuilder Pro to have access to everything you need for sequence editing and annotation in one easy-to-use application.

Lasergene Molecular Biology Applications

SeqBuilder Pro

Sequence Editing, Cloning, and Primer Design

SeqBuilder Pro provides sequence analysis tools for effortless sequence editing and annotation, plasmid map creation, in silico cloning and PCR primer design.

MegAlign Pro

Multiple Sequence Alignments

MegAlign Pro performs multiple sequence alignments quickly and easily, then guides you through the post-alignment process, including thorough phylogenetic analysis.

SeqMan Ultra

Sanger Sequence Assembly and Analysis

SeqMan Ultra accurately assembles Sanger ABI sequencing data with or without a reference, and includes an easy-to-use interface for previewing and trimming trace data.

GeneQuest

Gene Discovery and Gene Annotation

GeneQuest offers a comprehensive set of analytical methods to facilitate finding and annotating the genes and regulatory elements on a sequence.

SeqNinja

Automated Sequence Editing Utility

SeqNinja makes it easy to edit large groups of sequences and annotations simultaneously using customizable templates for functions such as translation and format conversion.

GenVision

Genome Illustration Utility

GenVision supports the generation of customizable publication-quality graphics for linear or circular genome mapping.

Compare DNASTAR Lasergene Packages

	Lasergene Molecular Biology	Lasergene Genomics	Lasergene Protein	DNASTAR Lasergene MOST POPULAR
Included Applications
SeqBuilder Pro	√		√
SeqMan Ultra	√	√		√
MegAlign Pro	√			√
GeneQuest	√			√
GenVision	√			√
SeqNinja	√			√
SeqMan NGen		√		√
ArrayStar		√		√
GenVision Pro		√		√
Protean 3D (+1 prediction per Nova Application)			√	√
DNASTAR Navigator	√	√	√	√

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