The base directory

• make a directory listing of downloads/ViennaRNA-2.1.1/

    $ ls -F ~/Tutorial/downloads/ViennaRNA-2.1.1/
  

	acinclude.m4   config.h.in     H/                 Makefile.am  Readseq/
	aclocal.m4     config.log      INSTALL            Makefile.in  RNAforester/
	AUTHORS        config.status*  INSTALL.configure  man/         RNAlib2.pc
	ChangeLog      config.sub*     install-sh*        misc/        RNAlib2.pc.in
	Cluster/       configure*      Kinfold/           missing*     stamp-h1
	compile*       configure.ac    lib/               NEWS         THANKS
	config/        COPYING         libsvm-2.91/       Perl/        Utils/
	config.guess*  depcomp*        m4/                Progs/
	config.h       doc/            Makefile           README

You now see the contents of the ViennaRNA-2.1.1 folder. Directorys are marked by a "/" and the "*" indicates executable files. The Makefile contains the rules to compile the code, the Perl folder and the Progs folder hold all the binaries but Kinfold and RNAforester and Utils contains the perl scripts. configure handels distinct options for installation and creation of the Makefile. INSTALL covers installation instructions and the README file contains information about the ViennaRNA Package.