This is a program to determine gene presence/absence variation based on read alignments to a reference genome and a gff3 gene annotation file.

INSTALLATION

git clone https://github.com/jdmontenegro/PAV.git
cd PAV
current=`pwd`
cd $HOME/bin
ln -s ${current}/pav.py .

Now you can call the script from anywhere in your system. Just make sure that $HOME/bin is in your PATH. If you do not know how to do this, this is the right time to ask for help to the system admin or google this out.