Downloading and Compiling ir

A program implementing sequence analysis based on the I_r is freely available under the GNU General Public License. The following instructions for using this software are based on a computer running the LINUX operating system. However, with a bit of tweaking they should also be applicable to other platforms.

Unpack ir

tar -xvzf ir_xxx.tgz

and change into the resulting directory

cd Ir_xxx

Compile the program by typing

make

The command

./ir -h

should now print the following list of program options:

ir version 2.3, copyright (c) 2006-2007 Bernhard Haubold & Thomas Wiehe
        distributed under the GNU General Public License.
purpose: calculate the index of repetitiveness, I_r
usage: ir [options]
options:
        [-i <FILE> read input from FILE; default: FILE=stdin]
        [-o <FILE> write output to FILE; default: FILE=stdout]
        [-w <NUM> sliding window of width NUM; default: no sliding window]
        [-c <NUM> increment sliding window by NUM positions; default: window_width/10]
        [-n <NUM> print NUM characters of header; all if NUM<0; default: NUM=30]
        [-s treat each sequence separately; default: union]
        [-p print information about program]
        [-h print this help message]