UNAFold v3.8

by Nick Markham & Michael Zuker
© 2006 Rensselaer Polytechnic Institute
Troy, NY 12180

The UNAFold package contains several programs for performing energy minimization
and partition function calculations on nucleic acid sequences.  Among the
programs is a Perl script, hybrid2.pl, which simulates a one- or two-sequence
ensemble of species by running other programs as appropriate.  hybrid2.pl is
thus the recommended command for most purposes.

The software is known to build and run properly on the following platforms:

Linux
FreeBSD
SGI IRIX
Sun Solaris
IBM AIX
MS Windows (with MinGW or Cygwin)
MacOSX 10.3

Building and installing the software should be as simple as typing ./configure,
make and make install.  By default, the software is installed in /usr/local/bin,
/usr/local/man and /usr/local/share, but this can easily be modified with the
--prefix option of the configure script.  For example, ./configure --prefix=~
will install the software in the user's home directory.

On many systems, performance can be increased significantly if certain compiler
flags are used.  For example, on a machine with an Intel Pentium III processor,
type ./configure CFLAGS='-O3 -march=pentium3' to enable Pentium III-specific
optimizations as well as architecture-independent optimizations.

The file INSTALL for more detailed information about the usage of the configure
script.  In addition to the options described therein, the configure script for
UNAFold supports the following options:

--enable-force enables support for force constraints.  Force constraints are
enabled by default, so there is no reason to use this option.  However, force
constraints may be *disabled* with --enable-force=no or --disable-force.
Disabling force constraints causes the software to run faster.

--with-apple-opengl-framework is usually required to build hybrid-plot on MacOS X.

--with-gd can be used to specify a non-standard location for the gd library.
--without-gd disables the usage of gd even if it would be found otherwise.
