redo_mlrgd and redo_plots

You can use these two scripts to redo the mlrgd and plots parts (respectively) of run_mlrgd, with different parameters. This is a lot quicker than rerunning all of run_mlrgd. Usage is

> ./redo_mlrgd prefix tttmin tttmax tVfit maxiter fitwhat refpos circular wholeseq range1 range2 Vfix Vtype Vmin Vmax skip newprefix

and

> ./redo_plots prefix window1 window2 circular clip1 clip2 newprefix

The new output files take the prefix newprefix.

You can experiment with the window sizes, and clipping parameters. For example, if you are looking for unusually conserved columns, then you aren't interested in highly variable columns so you may want to set clip2 quite high (e.g. 50%, provided the window size is sufficiently large) so that such columns don't contaminate conserved columns in the same window. On the other hand, if the typical length of features that you are interested in is 10 nt, then you could set the window size to 10 nt (e.g. window1 = 5).