Index of /downloads/oxbench
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,
tar zxvf 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:
(the full documentation is in docs/oxbench.pdf)
then build the libblocfile library:
then build oxbench
set the OXBENCH environment variable (e.g. with csh):
setenv OXBENCH ./
test the metrics:
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
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
for details of how the benchmark suite was developed and its application.
Geoff Barton 21st June 2005