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