SIFT4G

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

Requirements

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

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

Installation

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’.

Usage

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

Check installation

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