Major PhyML parameter "Gamma shape parameter" in UGENE GUI corresponds to command line option "-a", parameter "Proportion of invariable sites" corresponds to option "-v".
Both "-a" and "-v" can take either a numerical value or value "e" as input. The "e" value states to get the maximum likelihood estimate.
However, in UGENE GUI there is currently no "e" value in the parameters list of values. Instead, as described in the parameters tooltips, UGENE should set the "e" value for the parameters, if their check boxes are unchecked. The problem is that it doesn't happen in UGENE 1.26.2.
Modify the GUI so that the "e" value is set more explicitly. Don't forget to update the tooltips.
