When a protein is bigger than 3276 aa's,
matplotlib can not plot it due to 2^16
horizontal pixel size limit. I changed
plotGEMMEmatrix function and the way I
call it to solve this problem. Now, the
program will divide big proteins into
500 aa chuncks and plot it in that way.

--verbose option controls if epistatic and independent
results files will be written or not. It is False by
default and therefore, the files are not written.

Convert trace->tjet, maxhalftracepchalftracecvhalfcvpc->max
and ssjetormax->sstjetormax in ESGEMME.