Running EMBOSS on Windows

The EMBOSS package (European Molecular Biology Open Software Suite (2000) Rice, P. Longden, I. and Bleasby, A) currently does not function on the Windows operating system as it was designed solely for compatibility with UNIX based systems. To allow the use of much of the emboss functionality it is possible to use the partially ported version of EMBOSS such as EMBOSSwin by Andre Blavier which currently offers 165 of the emboss programs, like EMBOSS this port can be interfaced with the Staden Package to provide a more graphical interface however some adjustments are required as detailed below.


Download the Newest Version of EMBOSSwin coded by Andre Blavier from his website.

The installation is intuitive, but the default install directory is your root directory, not program files — you may want to change this, whichever directory you choose take note of it for future stages.


The Staden package although no longer in active development is still available for free download at their Sourceforge.

For the purpose of this guide, you’ll need to download the Windows version of the program (obviously). For those of you feeling lazy, this link leads to the downloads section.

Making them work together

To allow Staden and EMBOSSwin to function together correctly you need to add an environment variable referencing EMBOSS_DATA to the installation route of EMBOSSwin (default is C:\EMBOSSwin) \data.

If you’re using Windows XP/2000 go into Settings -> control panel -> System. Advanced -> Environment Variables. Then click the New bottom near the bottom of the screen, you will be asked for a variable name and variable value. For the name, you should type “EMBOSS_DATA” (without the quotes) for the value you should type your EMBOSSwin installation directory followed by (without any spaces) “/data” (again no quotes). Now Spin should be able to access your EMBOSSwin installation without a problem.

Additional points of interest

The way in which EMBOSSwin accesses databases by default can be inconvenient for the needs of an average user to give greater srs support to a wider array of databases you can use our alternative “emboss.ini” file simply download it from the link below and overwrite the existing emboss.ini file stored in the installation root of EMBOSSwin with this version.

Download the ini file here

Some antiviruses may complain about the file, just ignore them.