CCB » CBCC » DupLoCut

About DupLoCut

DupLoCut computes ancestral gene orders, given a phylogenetic tree and gene orders assigned to the leaves of the tree. It attempts to find the most parsimony assignment of gene orders under the duplication-loss evolutionary model.


Getting DupLoCut

This software is OSI Certified Open Source Software .

Click here to download the latest version of DupLoCut. To extract files to the current directory type:

% tar -vxzf DupLoCut.tar.gz 

The software was developed and tested on a Linux x86_64 system. It uses CPLEX 12.4, whose license is required to run DupLoCut. DupLoCut has been developed using an academic license from IBM.


Running DupLoCut

% DupLoCut -i <tree-file> -g <genome-file> -o <output-prefix>

For a more detailed description see the README file or type

% DupLoCut --help


Example Instance

Stable tRNA and rRNA of 12 Bacillus lineages from amyloliquefaciens, subtilis, thuringiensis and cereus. Download RNA orders and NCBI taxonomy in format suitable for DupLoCut. The ancestral gene orders computed by DupLoCut imply 120 duplication and loss events.


References

Our paper describing DupLoCut will be uploaded as soon as it is accepted for publication.


Funding

This work is supported in part by NIH grant and R01-HG006102 to S.L. Salzberg.