NCCD
Programs to compute the NCCD (Normalized Conditional Compression Distance) and perform phylogenomics (whole genome) on 48 bird species. It will use a state-of-the-art genomic compressor, based on a mixture of finite-context models, as a metric distance.
INSTALLATION
Simply run:
wget https://github.com/pratas/NCCD/archive/master.zip unzip master.zip cd NCCD-master
EXECUTION
Make shore you have at least 200 GB of space in the hard drive. Then, simply run:
. run.sh
It will download and install GeCo (https://github.com/pratas/geco/), although it might be needed to install cmake. Then, it will download all the the 48 bird sequences and run the NCCD.
For other purposes, such as a simple information distance between two sequences (fileA and fileB), go to scripts:
cd scripts
and run
. NCCD.sh ../examples/fileA ../examples/fileB
It will calculate the NCCD on two synthetic sequence examples included in the system.
ISSUES
For any issue let us know at issues link.
LICENSE
GPL v2.
For more information:
http://www.gnu.org/licenses/gpl-2.0.html