Software for DNA, RNA and Cloning


It says: The award winning 4Peaks helps molecular biologists to visualize and edit their DNA sequence trace files.

License: Freeware


It says: Amplify is a freeware Macintosh program for simulating and testing polymerase chain reactions (PCRs). It can also be used as a tool for designing primers by evaluating candidates.

License: Freeware


You can use it for viewing DNA sequence, translation, creating graphic restriction maps, saves graphics as encapsulated postscript or scalable vector graphics, virtual restriction digest and a lot more.

License: Freeware

Beacon Designer

It says: Beacon Designer™ automates the design of real time primers and probes. You can BLAST search sequences and search for template structures from within the program. Beacon Designer™ offers a comprehensive solution for mutation detection. Use Beacon Designer™ for optimal TaqMan® probes. And a lot more.

License: Commercial, free Trial


It says: Design, analyze, and share sequence data in the cloud.

License: Commercial, free online demo


It says: BioSAVE (the E probably comes from Viewer somewhere) is a program for visualising DNA or protein sequences and annotations thereof.

License: Freeware, Source code available as Xcode project

CLC Genomics Workbench

It says: CLC Genomics Workbench, for analyzing and visualizing next generation sequencing data, incorporates cutting-edge technology and algorithms, while also supporting and integrating with the rest of your typical NGS workflow.

License: Commercial, free Trial

CLC Sequence Viewer

It says: CLC Sequence Viewer creates a software environment enabling users to make a large number of bioinformatics analyses, combined with smooth data management, and excellent graphical viewing and output options.

License: Commercial, free Trial


It says: Free online software tools and information resources for molecular cloning.

License: Free online tools

Clustal X

It says: Multiple alignment of nucleic acid and protein sequences.

License: Freeware

CodonCode Aligner

It says: CodonCode Aligner is a program for sequence assembly, contig editing, and mutation detection.

License: Commercial, free Trial

DNASTAR's Lasergene Cloning Suite

It says: Lasergene Cloning Suite software enables you to edit and annotate your sequences, create detailed circular or linear maps, perform automated virtual cloning using a variety of cloning methods, including Gateway multisite, TA, TOPO, and restriction cloning, and also provides all the tools you need for designing the best primer pairs for PCR, sequencing, and hybridization experiments.

License: Commercial, free Trial

DNA Strider

It says: An intuitive and handy utility that helps its users to quickly get their data out and perform some basic DNA analysis functions.

License: Freeware


It says: EnzymeX helps molecular biologists determine which restriction enzymes they should use to cut their DNA of interest, along with complete DNA sequence analysis and editing.

License: Freeware


It says: For the viewing of ABI and SCF chromatogram files.

License: Freeware


It says: A highy interactive molecular biology software to analyze sequences.

License: Freeware, but based on Java

Gene Construction Kit

It says: GCK allows easy manipulation of DNA sequences, either graphically or as sequence text. GCK eliminates tedious examination of DNA sequence data by automatically identifying open reading frames (ORF's), keeping track of sticky ends during cutting and pasting of restriction enzyme digestion fragments, assisting with PCR primer design, and enabling comprehensive annotation of DNA sequence features.

License: Commercial, free Trial


Beautiful sequence alignment, assembly and analysis software for DNA and protein sequence alignment, genome browser, reference mapping and sequence assembly, Phylogenetic Tree Building and Viewing, molecular cloning, primer design, microsatellite genotyping and more.

License: Commercial, free Trial, based on Java


It says: Gene Studio is a free tool for modelling of DNA manipulation. It will allow to work with vectors, to design primers, to clone molecules and provide user friendly interface.

License: Freeware, source code available

Lasergene Genomics Suite

It says: Lasergene Genomics Suite provides all of the software you need for next-gen sequence assembly and analysis in a single, integrated package. We support all major next-gen sequencing technologies, making it simple to work with your data for any type of project, including de novo or reference-guided genome assemblies, targeted resequencing, metagenome and population assemblies, large-scale multi-sample SNP analysis, RNA-Seq, ChIP-Seq, and miRNA alignment and analysis, and more.

License: Commercial, free Trial


It says: MacVector is a comprehensive Macintosh application that provides sequence editing, primer design, internet database searching, protein analysis, sequence confirmation, multiple sequence alignment, phylogenetic reconstruction, coding region analysis, and a variety of other functions.

License: Commercial, free Trial


It says: OLIGO Primer Analysis Software is the essential tool for designing and analyzing sequencing and PCR primers, synthetic genes, and various kinds of probes including siRNA and molecular beacons. Based on the most up-to date nearest neighbor thermodynamic data, Oligo's search algorithms find optimal primers for PCR, including TaqMan, highly multiplexed, consensus or degenerate primers. Multiple file batch processing is possible. It is also an invaluable tool for site directed mutagenesis.

License: Commercial, free Trial


It says: PlasmaDNA is a new, free DNA analysis and manipulation software. It is simple to learn and to use, and contains multiple features designed to help with the design of a successful cloning strategy, the generation of the sequences of new clones, the archiving of the cloning strategy.

License: Freeware

Sequence Analysis

For analysing sequences

License: Freeware, but based on Java

Serial Cloner

It says: All the tools you need to analyze and manipulate your sequences are available in an all-in-one-window concept. Numerically select fragments, find restriction sites, ORF or any nucleotide or peptide sequence, calculate Tm of selected fragments, %GC or dynamically determine the translation your selection into peptide and calculate the MW using a compact interface.

License: Freeware


It says: SnapGene offers the fastest and easiest way to plan, visualize, and document your molecular biology procedures.

License: Commercial, free Trial and free Viewer

Unipro UGENE

It says: Creating, editing and annotating nucleic acid and protein sequences. Multiple sequence alignment. Cloning in silico. Search for direct, inverted and tandem repeats in DNA sequences. Integrated Primer3 package for PCR primers design. Restriction analysis with integrated REBASE restriction enzyme database. And more.

License: Freeware, Source code available

Vector NTI® Express

It says: Vector NTI® software is a completely integrated suite of sequence analysis and design tools that help you manage, view, analyze, transform, share, and publicize diverse types of molecular biology data, all within one graphically rich analysis environment.

License: Commercial, free Trial


The author: WebDSV is a free online DNA sequence editor and map/plasmid drawing program.

License: Free online tool


It says: It draws plasmid or linear DNA maps, showing features such as genes, multiple cloning sites, and restriction sites.

License: Freeware