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UGENE Portable 40.1

A free software designed for use in bioinformatics

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UGENE Portable screenshotUGENE is a free and powerful bioinformatics application which is able to support several platforms and which can be installed with only a few mouse clicks.

By using UGENE you will be able to create, annotate and edit protein sequences and nucleic acid. the application supports several sequence alignment, such as ClustalO, MUSCLE, T-Coffee, ClustalW, Kalign, MAFFT, etc. Moreover, the program allows you to search through a wide range of online databases, including UniProtKB / Swiss-Prot, UniProtKB / TrEMBL, NCBI, PDB, DAS servers, and many more.

UGENE integrates the Primer3 package, allowing you to create PCR primer designs. Plasmid annotation and construction is also possible. Moreover, the program integrates a powerful enzyme finder containing a REBASE restriction enzymes list. HMMER2 and HMMER3 packages are included as well.

UGENE allows you to process raw NGS data and lets you perform complex RNA-seq and ChIP-seq data analysis. In addition, the application lets you view and analyze BAM files via the UGENE Assembly Browser.

UGENE is able to create and edit phylogenetic trees by using PhyML Maximum Likelyhood, PHYLIP Neighbor Joining or MrBayes. A chromatogram viewer viewer is included for making your work easier.

By using UGENE you will be able to easily search for inverted, direct or tandem repeats in a DNA sequence. The included UGENE Workflow Designer allows you to easily mix various algorithms in order to create custom workflows. The program also integrates the GOR IV and PSIPRED algorithms which will help you with protein secondary structure predictions.

The UGENE Query Designer lets you search for patterns of distinct algorithms in a nucleic acid sequence. Construction of dotplots for nucleic acid sequences is possible as well.


  • The application does not require installation.
  • Supports several sequence alignment.


  • The application requires a certain level of knowledge in the Bioinformatics field.
  • Some features require a graphics card that supports CUDA technology.
Name UGENE Portable
Version 40.1
Developer | see all products from this developer
Product Homepage UGENE Portable
License Free (Freeware)
Last Week Downloads 5
All Time Downloads 1,234
Filesize 352.9MB
MD5 Checksum 327D307F2E1F65CC07792EAC9EBD6D43
OS Support Windows All
Category Home & Education

100% CLEAN Certification

BadgeUGENE Portable has been tested by team against viruses, spyware, adware, trojan, backdoors and was found to be 100% clean. Our editors will recheck this software periodically to assure that it remains clean.


Old Versions

Software Date Added
UGENE Portable 40.1 October 12, 2021 - Latest Version
UGENE Portable 1.33.0 October 01, 2020
UGENE Portable 1.26.1 February 24, 2017

Download the free UGENE Portable