Institute of Computer Science
University Freiburg



You can try to run MARNA on your local machine. I have written a preliminary version which is executable on my machine and hopefully on your machine as well. I use a 2.8 GHz Pentium IV machine, kernel version 2.6. OS: Suse Linux 9.2. If you have a similar machine and if you have installed T-Coffee, the RNA Vienna Package and RNAshapes then the chances are great that MARNA runs fully on your local machine.

  • Install tcoffee such that it can be run globally from any directory
  • Install Vienna RNA package (RNAfold/RNAsubopt) and/or RNAshapes such that it can be run globally from any directory
  • Download MARNA-100729.tar.gz.
  • Unpack it with 'tar -xzf MARNA-100729.tar.gz'
  • Change the unpacked source directory with 'cd MARNA'
  • Check install notes and further information in file 'INSTALL.readme' (e.g. with 'less INSTALL.readme')
  • Compile with 'make'
Then test it with './ test.efasta'.

Reports are welcome !

If something seems to be wrong, then don't hesitate to write an email to : rna[ @ ]

Please cite :
Sven Siebert and Rolf Backofen,
"MARNA: multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons",
Bioinformatics 2005, Volume 21, Issue 16, 3352-3359

Update history:
  • 2010-07-29 : Martin Mann : source updated to compile with g++ 4.3.4
  • 2006-02-24 : Sven Siebert : initial source package