SPiTDRL Downloads

CREx2 can be downloaded here.

1. Download SPiTDRL
2. Extract SPiTDRL.tar.gz (tar -zxvf SPiTDRL.tar.gz)
3. If no Linux distribution is used compile the SPiTDRL source code using the given Makefile. Otherwise, no further installation is needed.

SPiTDRL is executed from the command line using:
./SPiTDRL -f <input file> [options]
use -h for more information.

The options of SPiTDRL are:
-f: fasta file containing (possibly multiple) gene orders,
-d: print only a table with iTDRL distances,
-h: prints help message,
where “-f” is a required argument.

For testing whether or not SPiTDRL is installed correctly enter:
i) ./SPiTDRL -f example.fas or
ii) ./SPiTDRL -f example.fas -d.

The first command produces two minimum length scenarios of iTDRL rearrangements that transform the given gene orders Start and Target (see example.fas) into each other.
The second command produces a table illustrating the iTDRL distances of the given gene orders Start and Target, i. e., the minimum numbers of iTDRLs necessary for such transformations.
The expected output is given in the README file.

Feel free to send bug reports or any other kind of impressions or suggestions on SPiTDRL to thartmann@informatik.uni-leipzig.de.