resources
If you are interested in mutation interpretation, see Alamut features.
If you are interested in NGS variants annotation, see Alamut-HT features.
embosswin
EMBOSSWin is a Windows port of EMBOSS, a free Open Source software analysis package specially developed for the needs of the molecular biology user community.
Please note that there is now a Windows port of EMBOSS provided by the EMBOSS team.
EMBOSS on the Windows platform
This work is an attempt to make the EMBOSS package run on Windows PCs. EMBOSS is a free open source software set of high-quality sequence analysis programs mainly designed for the Unix operating system.
The ambition of this work is to provide an easy-to-install and easy-to-use EMBOSS distribution for the Windows platform (NT, 2000 or XP).
Current version (2.10.0-0.8 - February 2005)
This is a port of version 2.10.0. It contains 165 command-line programs out of the reference Unix distribution.
What's new in this release?
- See the log file of changes at the Emboss web site.
- eprimer3 is now in the distribution (but emma and tfm are not).
- Fixed a bug in garnier (thanks to Scott Markel).
- Emboss databases and programs can now on some systems be accessed from Windows Staden spin. Under which circumstances this is possible remains to be elucidated. Help and suggestions on this topic would be appreciated.
25 June 2005: The installer now sets the EMBOSS_DATA environment variable for better Staden compatibility. The default emboss.ini file has also been changed, with entries for a number of SRS databases. (Thanks to David Judge)
Previous versions
- Version 2.7.1-0.7 - September 2004: Fixed problems with sequence alignment programs.
- Version 2.7.1-0.6 - February 2004: Fixed a bug in pepstats (thanks to Olivier Collin)
- Version 2.7.1-0.5 - October 2003: Port of EMBOSS version 2.7.1
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Version 2.6.0-0.4 - September 2003:
- Windows paths (e.g.: C:\data\xlrhodop.pep) can now be used for output sequence parameters (thanks to Geetha Vasudevan who pointed this out).
- lindna and cirdna used to crash (thanks to Lothar Prix who reported this). They should now behave more politely, although I'm not sure the problem has been fully solved.
- Version 2.6.0-0.3 - 10 May 2003: contains 152 command-line programs out of the reference 2.6.0 Unix distribution. emma, eprimer3 and tfm are not part of this package. The ajax and nucleus libraries are now built as DLLs, so each program is now much smaller, as the whole package is.
Installing and running
(EMBOSS for Windows doesn't work on pre-NT OSs, i.e. 95, 98, ME)
Download and install the self-extractible package: embosswin-0.8-setup.exe After installing, you can use the programs through a DOS command prompt, much like you do under a Unix shell. EMBOSS configuration (variables and databases) is defined in the emboss.ini file, located in the installation directory.
For details on how the installer affects your system, look here.
Technical details
This package has been built with Visual C++ 7.1 (aka VC++ 2003) and the PLPLOT library version 5.1.0. It should run on Windows 2000 & XP.
More technical information about this build and a source code distribution are available.
Legal section
Open source. GPL, LGPL. This product includes software developed by the Whitehead Institute for Biomedical Research (primer3_core).See Copyright-primer3.txt in the distribution
