Any sequence of symbols stored as 'sequence associated information' ('SAI') can be selected from the 'Select a Filter' subwindow and used as a filter for the in or exclusion of alignment columns for treeing. If any species is selected, you may use it's sequence for filter. It's name will be displayed just before the SAI names.
The characters of the filter which define columns to exclude have to be defined in the respective input field.
Additionally or alternatively you may define the absolute column range to be used (a range from 0 to 0 means 'use whole sequence').
The selected filter is displayed in the subwindow on the bottom.
All bases may be simplified, leaving only transversions and simplified amino-acid-groups, allowing transversion parsimony/fdnaml/distmethods