This is the distribution package for gapwm, a genetic algorithm
for optimizing a position weight matrix (PWM).

Position weight matricies are simple models commonly used in 
motif finding algorithms to identify short functional elements,
such as cis-regulatory motifs, on genes.  When few expermentially
verified motifs are available, estimation of the PWM may be poor.
gapwm implements a simple method to improve a poorly estimated PWM
using chromatin immunoprecipitation (ChIP) data.

This program was developed by Leping Li of the National Institutes
of Environmental Health Sciences, Research Triangle Park, North
Carolina 27709.

LICENSE

This work is made available under the GPL v2.

BUILDING

In the main directory of the distribution, type 

./configure

then 

make
make install

By default, the configure program will direct the executable files
to /usr/local/bin which, in most cases, requires the user to "su" to 
root prior to the "make install" step.  The target directory for the 
executable file can be overridden by specifying the --prefix option
during the configure phase.  For example, 

./configure --prefix=/home/gapwm_user

will direct the executables into /home/gapwm_user/bin directory.  

The configure application accepts several arguments to tailor the
build and installation process.  Please see the INSTALL file contained
in the root directory of the distribution for further details.

