Before compiling, make sure that the following libraries and headers
are installed:
the Glib library version 2, part of the GTK toolkit (http://www.gtk.org)
    (standard on most systems; version 1 should also work if you manually 
    create the Makefile)
the GNU Scientific Library (http://sources.redhat.com/gsl)

If using debian or RPM packages, make sure to install the header
packages (gsl-devel, glib2-devel).  Both libraries should be
compilable from source on most unix systems.

----------------------------------------------------------------------
AUTOMATIC COMPILING

If the libraries are installed in standard places, the following
should be sufficient to compile and install PhyloGibbs:
   ./configure
   make
   make install

This installs PhyloGibbs in /usr.  In particular, the phylogibbs
binary goes into /usr/bin and the manpages into /usr/man/man1 and
/usr/man/man7.  To install it elsewhere, eg in /opt or in your home
directory, use ./configure --prefix=/opt or --prefix=$HOME .  To
uninstall, type "make uninstall" (without reconfiguring, or after
configuring with the same prefix).

If the GSL and Glib libraries and headers are in nonstandard 
places, set appropriate CPPFLAGS and LDFLAGS variables: eg,
export CPPFLAGS="-I/opt/include"  (csh: setenv CPPFLAGS "-I/opt/include")
export LDFLAGS="-L/opt/lib"       (csh: setenv LDFLAGS "-L/opt/lib")
before running the configure script.

--------------------------------------------------------------------
MANUAL COMPILING

If the above fails, or if you don't like GNU Autoconf, cd to the src
directory and copy the file Makefile.manual to Makefile.  You may need
to customise it: in particular, set the PREFIX variable to what you
want, add any necessary paths to CLIBS (eg, -L/opt/lib) and CINCLUDES
(eg, -I/opt/include).  Then type "make" and the binary should be 
compiled. 

On recent systems, you may be able to obtain the appropriate flags 
for glib with
pkg-config --cflags glib*

Leave in the -DDEBUG option: this turns on various internal
consistency checks, and the slowdown is negligible (especially
compared to the added peace of mind).

Having done all this,
   make
will compile the program (the binary is called "phylogibbs")
   make install
will install it in $(PREFIX)
   make deinstall
will remove it from $(PREFIX)

Instead of "make install", you can just run it (and read the manual
pages) from the source directory, or copy the binary and the two
manual pages by hand to the desired location.

-----------------------------------------------------------------------

This program has been extensively tested on Linux, FreeBSD and
DragonFly (a recent FreeBSD variant).  It will probably work on other
Unix-like systems (including MacOS X) if the above libraries are
installed, and may also work on Windows under CygWin, but has not been
tested on any of these systems.
