Installation:

This package uses GNU autoconf generated configure scripts, see the
file INSTALL.configure for generic configure documentation.

Quickstart: Usually you'll just have to type:
----------
	./configure
	make
and (as root)
	make install 

Install Paths:
-------------
RNAcop uses the functions, etc. from the ViennaRNA package, but creates its own copy of 'libRNA.a', 'libRNAcop.a'. The main programs, library, man, and info pages are
installed in the usual places by default
(i.e. /usr/local/{bin,lib,man,info}). In addition the following
install paths are used:
header files	/usr/local/include/RNAcop	[includedir/RNAcop]
parameter files	/usr/local/share/RNAcop      [datadir/RNAcop]

All these locations can be changed by calling ./configure with
appropriate options.

If you like having all software packages separated in their own directories
you could run e.g.:
./configure --prefix=/opt/packages/RNAcop --datadir=/opt/packages/RNAcop 
resulting in /opt/packages/RNAcop/{bin,lib,man,include} directories

General remarks:

Calculating the partition function for long sequences ( >400 bases)
generates a lot of floating point underflows. On some system this can slow
down the calculation dramatically because an exception is invoked for each 
underflow. How to avoid this problem is highly system specific:

On SunOS 4.1 the remedy is calling nonstandard_arithmetic() add a -DSUN4 to
the CFLAGS in lib/makefile to do this. Use CC=gcc since SUN's standard cc
doesn't understand ANSI C.

On HP machines running hpux-9 or hpux-10 add -DHP9 to the CFLAGS so that
fpsetfastmode() will be called.
