Besides selecting an appropriate package for your operating system (Windows, Mac OS X, or Linux; 32 or 64 bit), you should take into account the following considerations.

Should I download standard, full, or NGS package?

Short answer: In most cases the full package is the best choice. Exceptions are:

• Use the standard package, if:
  • You're going to use only basic UGENE features and don't want to waste Internet traffic
  • You have limited disk space
• Use the NGS package, if:
  • You're going to analyze ChIP-Seq data with the Cistrome pipeline

Detailed answer: Some tools are embedded into UGENE as external. This means that such tool needs an external executable to be launched from the UGENE graphical interface. The standard package does not include such tools, 

I have Windows. Should I download installer package or portable zip bundle?

If you have administrative rights on Windows, use the installer package. It will make integration with your Windows system more tight. For example, it will add associations for bioinformatics formats supported by UGENE, so that corresponding files are opened in it by default.

I have Linux. Which package should I use?

There is

If you're an Ubuntu user, follows this guide to install UGENE on your system.