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?
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
Explanation of the tip above: Some tools are embedded into UGENE as external. To be launched from the UGENE graphical interface, an external tool needs a corresponding executable file. The list of the external tools can be found on this page.
The standard package does not include the tools, whereas the full package include all the required tools.
The NGS package, besides containing the external tools, contains sample data for the Cistrome pipeline (hg19 genome, reference genes, etc.), so you can run it out of the box.
In 2013 we worked on extending of the UGENE NGS framework with three popular pipelines for analyzing NGS data:
The NGS package was added as the result of this work. We decided to add it as we want our users to be able to use all UGENE features out of the box. However, it appears that the first two pipelines are also available out of the box in the full UGENE package 
The work was supported by grant RUB1-31097-NO-12 from NIAID.
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?
If your Linux is not Ubuntu or Fedora, then universal binary package is the only choice. Otherwise, for more tight integration with the systems, you can install UGENE from corresponding repositories, following these guides:
Please note that the repositories may be updated a little later the official UGENE release date.