SIFT (Sorting Intolerant From Tolerant) For Genomes (http://www.nature.com/nprot/journal/v11/n1/full/nprot.2015.123.html)

• g++ (4.9+)
• GNU Make
• nvcc (2.*+) (optional)

*note: It was only tested on Linux (Ubuntu 14.04).

To build SIFT4G run the following commands from your terminal:

git clone --recursive https://github.com/rvaser/sift4g.git sift4g
cd sift4g/
make

Running the 'make' command will create the bin folder which contains the sift4g executable.

Troubleshooting

If you accidentally left out '--recursive' from git clone, run the following commands before running 'make':

git submodule init
git submodule update

Optional

If you have a CUDA enabled graphics card (and the nvcc compiler) run 'make gpu' instead of 'make'.

To run the default version of SIFT4G run the following command:

./bin/sift4g -q <query .fa file> -d <database .fa file>

where both the query and database files are protein sequences in fasta format.

To see all available parameters run the command bellow:

./bin/sift4g -h

To test sift4g, go to the test_files directory and follow directions in README