Page History

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• BLAST, Smith-Waterman - popular basic local sequence alignment tools.
• HMMER2/HMMER3 - sequence analysis using profile hidden Markov Models constructed from multiple sequence alignments.
• ClustalW, ClustalO, Muscle, K-Align, Mafft, T-Coffee multiple sequence alignment algorithms.
• Repeat finding and sequence comparison algorithms with a convenient dot-plot based results visualization.
• Open reading frames visualization and export.
• Restriction sites visualization tool with included version of REBASE database.
• Transcription factor binding sites analysis with SITECON, weight-matrix based algorithms and included version of JASPAR database.
• Short read aligners: BWA, Bowtie, Bowtie2, UGENE Aligner.
• GC-content, AT-content graphs.
• Mr bayes and Phylip tools for phylogenetic trees construction.
• ... and dozens of other popular and highly cited tools.

Hardware requirements

• UGENE runs smoothly on almost all hardware available: single core Pentium III or higher computer with 200Mb of free disk size and 256Mb memory is enough.
• Use UGENE on Mac, Windows or Linux operating systems. Both 32 and 64 bit versions are available.
• No 3rd-party software is needed to be installed to use UGENE!
  The system requirements for UGENE are these:
  • Operating system (32 or 64 bit):
    
    • Windows XP, Windows Vista, Windows 7, Windows 8
      ^{Using a zip package it is possible to use UGENE without administrative rights on Windows}
    • Mac OS X 10.5 or later
      ^{For older Mac OS X versions (PowerPC, 10.4) UGENE version 1.10.3 is avaialble.}
    • Linux
      • Ubuntu 12.04 or later
      • Fedora 19 or later
      • If you have another Linux system, you may use a universal binary package
        
        
  • RAM:
    

    • 512 Mb RAM required

    • 2 Gb RAM recommended

    
    
  • Disk space:
    Minimum required disk space depends on the UGENE package
    
    • Standard package: 200-300 Mb
    • Full package: 500-900 Mb
    • NGS package: 21-24 Gb
      
      
  • Display:
    • It is recommended to set the screen resolution to a value greater than 1280x1024.
      
      
  • Internet:
    
    • Internet connection is required for some tasks like loading data from online databases.
      
      

  Tip
  UGENE takes care to use capabilities of your system: the more RAM and cores you have, the more quickly you'll get results of your calculations. Also, if you have an OpenCL-capable video card, you can use GPU-optimized versions of the following tools: Smith-Waterman Search UGENE Genome Aligner

  In most cases it is recommended to use UGENE full package, as it embeds additional external tools, such as local BLAST, Bowtie, etc. When the full package is used, the external tools can be run out of the box.

  The list of the external tools and their availability for different operating systems can be seen on this page.

  For details about UGENE packages, see this page.

Customization and cooperation

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