Removed SC2 and SC2 calculations.

Since we are not using SC2 and SC3 calculations anymore in SGEMME, I decided to remove them. They were making the computations quite slow due to multiple external calls to JET. In addition, I updated the bash script in the examples directory. We have an example to calculate all possible single point mutations. Besides, we have an example to calculate only mutations of interest given in a blah-blah.mut file.

example/Stiffler_2015_BLAT_ECOLX.mut

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