DNA assembly software tools | Synthetic biology

Molecular biologists routinely clone genetic constructs from DNA segments and formulate plans to assemble them. However, manual assembly planning is complex, error prone and not scalable. Source text: Appleton et al., 2014.

Genome Compiler Genome Compiler

Genome Compiler

Provides the industry with a comprehensive platform for all your synthetic…

Provides the industry with a comprehensive platform for all your synthetic biology needs. You will benefit from direct connections to an array of DNA synthesis providers, lab facility services and an…

BioPartsBuilder BioPartsBuilder

BioPartsBuilder

A biologist-friendly web tool to design biological parts that are compatible…

A biologist-friendly web tool to design biological parts that are compatible with DNA combinatorial assembly methods, such as Golden Gate and related methods. BioPartsBuilder retrieves biological…

Web app
PromoterCAD PromoterCAD

PromoterCAD

A web application for designing synthetic promoters with altered…

A web application for designing synthetic promoters with altered transcriptional regulation. PromoterCAD is built on the LinkData open platform for data publication and rapid web application…

Desktop app
Web app
Raven Raven

Raven

Uses a sophisticated dynamic programming algorithm to design high-quality DNA…

Uses a sophisticated dynamic programming algorithm to design high-quality DNA assembly plans. Raven produces SBOL compliant images that visualize your assembly plan as well as human readable…

Desktop app
Pydna Pydna

Pydna

An extensible, free and open source Python library for simulating basic…

An extensible, free and open source Python library for simulating basic molecular biology DNA unit operations such as restriction digestion, ligation, PCR, primer design, Gibson assembly and…

Desktop app
ApE ApE

ApE

A software tool for viewing, editing and analyzing plasmid sequences.

A software tool for viewing, editing and analyzing plasmid sequences.

Web app
DeviceEditor DeviceEditor

DeviceEditor

Provides a graphical design environment that mimics the intuitive visual…

Provides a graphical design environment that mimics the intuitive visual whiteboard design process practiced in biological laboratories. The key innovations of DeviceEditor include visual…

Web app
Pigeon Pigeon

Pigeon

A web-based tool that translates a textual description of a synthetic biology…

A web-based tool that translates a textual description of a synthetic biology design into an image. Pigeon allows programmatic generation of design visualizations, is easy to learn, is easily…

Desktop app
Web app
R2oDNA Designer R2oDNA Designer

R2oDNA Designer

A web application that stochastically generates orthogonal sets of synthetic…

A web application that stochastically generates orthogonal sets of synthetic DNA sequences designed to be biologically neutral. Biologically neutral sequences may be used for directing efficient DNA…

Desktop app
QuickGene QuickGene

QuickGene

A molecular biology program for DNA analysis, assembly and cloning. Built by…

A molecular biology program for DNA analysis, assembly and cloning. Built by scientists for scientists, its goal is to be exceedingly user-friendly and intuitive, while making no sacrifices in…

Web app
j5 j5

j5

Automates the design of scar-less multipart DNA assembly protocols including…

Automates the design of scar-less multipart DNA assembly protocols including SLIC, Gibson, CPEC, and Golden Gate. The key innovations of the j5 design process include cost optimization, leveraging…

Desktop app
SimVector SimVector

SimVector

Performs restriction mapping, restriction analysis, plasmid map drawing,…

Performs restriction mapping, restriction analysis, plasmid map drawing, gateway, TA and restriction cloning.

Desktop app
G T A T C G C T A Geneious Geneious

Geneious

A powerful and comprehensive suite of molecular biology tools that provides…

A powerful and comprehensive suite of molecular biology tools that provides visual sequence alignment and editing, sequence assembly with a clear graphical interface, comprehensive molecular cloning…

Desktop app
Web app
CLONEQC Deprecated CLONEQC

CLONEQC

A lightweight software pipeline available as a free web server and as source…

A lightweight software pipeline available as a free web server and as source code that performs quality control on sequenced clones. Input to the server is a list of desired sequences and forward and…

Web app
GenoREAD GenoREAD

GenoREAD

A web-based application that breaks the sequence verification process into two…

A web-based application that breaks the sequence verification process into two steps: the assembly of sequencing reads and the alignment of the resulting contig with a reference sequence. GenoREAD…

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