[Sow]

Thanks.
Yes I tried that but that doesn't even run the configure step.
Both make and make install steps do not work.
And I do see a make file in the ViennaRNA package.

[mastal]

Actually, according to the manual,

http://www.tbi.univie.ac.at/RNA/documentation.html#install

the correct syntax is:

./configure --prefix=/home/username/ViennaRNA


What type of computer/operating system are you trying to install the software on?

If make doen't work, have you tried downloading the precompiled binaries, if there are precompiled binaries for your system?