Gblocks Questions

Jose,

I am including with this message the latest menu for running Gblocks from BioLegato. My goal is to convey to the user the meaning of the parameters, within the context of the task. There is a bit of an art to designing good menus. Since Gblocks operates in a series of steps, I have laid out the menu in the order of those steps. I have several questions:

a) Your paper from Mol. Biol. Evol. (2000) states "...conserved (>= IS and < FS)...".  Therefore command line parameters -b1 <= -b2 . I have set the defaults in the Gblocks menu to  51% and 85%, respectively. My question is, will it ever be reasonable for -b2 to be less than 85%? If so, what is a reasonable range for -b2, as a percentage? (As an aside, BioLegato passes these parameters to a custom Python script which does sanity checking on parameters and then submits the job to Gblocks. Since BioLegato has no way to know the number of sequences in advance, I have implemented these as percentages, and the Python script figures out how to set the number of sequences for -b1 and -b2.)

b) From your paper, I infer that -b6, use of similarity matrices, is only pertainant to -b1 and -b2. For this reason I have presented this option as indented to 1 and 2 in the menu. Correct me if I am wrong.

c) In all cases you are seeing the defaults presented to the user. Please suggest better defaults, if warranted.

d) Menu item 5 (-b5) is implemented as a pull-down chooser. I have tried to convey the meaning of these three choices, but let me know if you prefer different wording.

e) As you'll see, I haven't implemented some of the output options. In many cases, they are unnecessary because the alignment pops up in a new BioLegato window that lets the user run further steps. For parameters -n, -u and -k, I am not sure how useful they would be for the purposes of running Gblocks through BioLegato.

I am open to any suggestions for improvement you may have.