This directory contains the OXBench multiple alignment benchmark suite.
Please see the OXBench web pages for further details and reference to the 
publication in BMC Bioinformatics.

The benchmark suite is aimed at developers of multiple protein sequence
alignment methods and others interested in testing multiple alignment 
methods.  It is known to work on Linux under a variety of distributions.

To install the oxbench suite, download the oxbench_1_3.tar.gz file in this directory, 
unpack it:

tar zxvf oxbench_1_3.tar.gz
(alternatively, do:
 gunzip oxbench_1_3.tar.gz
 tar xvf oxbench_1_3.tar
)

MAKE SURE your computer has the pcre library installed.  You can get this 
from www.pcre.org, then:

change directory to the distribution:

cd oxbench_1_3

(the full documentation is in docs/oxbench.pdf)

then build the libblocfile library:

cd libblocfile
make

then build oxbench

cd ..
make install
make subsets

set the OXBENCH environment variable (e.g. with csh):
setenv OXBENCH ./

test the metrics:
make test

You should then set the OXBENCH variable appropriately for your system
and add the $OXBENCH/bin directory to your path.

See docs/oxbench.pdf for full details of how to use the benchmark suite
and see:

Raghava, G. P. S., Searle, S. M. J.,  Audley, P. C, Barber, J. D. 
and Barton, G. J. (2003), BMC Bioinformatics, 4:47
"OXBench: A benchmark for evaluation of protein multiple sequence
alignment accuracy".

for details of how the benchmark suite was developed and its application.


Geoff Barton 21st June 2005
---------------------------