Output of PhyML execution:
- use monospace font 
- scroll down to follow the progress of the execution

When GTR is on -> transition/transversion ratio option should be off.

Suppress the black horizontal lines separating the sub-sections

Replace PhyMLGuifiles/ by bin/ in PhyMLPanel.java


Replace #Subcategories by # of rate classes

Replace Gamma with Shape parameter and Alpha with Value

Boxes and buttons seem to be a bit all over the place. Is it possible
to justify them? For example, a starting point could be to set all
the boxes to the same width, same of the scrolldown menus.

Optimise Rate Parameter should be only active when the model
selected is GTR. When model=custom it should be set to 'yes'
with no option to change it.
