Phonology Assistant initially displays word lists ungrouped. A group of minimal pairs is a set of rows for which the phonetic data is similar in the search environments.
To group a word list by minimal pairs in the active search result tab, do one of the following:
On the View menu, click Minimal Pairs.
On the Search
toolbar or Distribution
Charts toolbar, click 
Minimal Pairs.
Each group heading displays the specific phonetic data in the search environments, followed by a list of the records in the group.
To view all the records
under the group headings, click 
Expand All Groups.
To view only the group headings,
click 
Collapse
All Groups.
To remove the groupings,
click Minimal
Pairs again.
The tab displays 
(Minimal Pairs Options)
so you can choose minimal pairs options.
Currently, the way the Minimal Pairs feature functions in Phonology Assistant, the program may produce pairs that are not phonologically minimal. For example, when searching for t/d minimal pairs, Phonology assistant would produce the following list:
[te] 'take' and [de] 'find', which are phonological minimal pairs. But [tu] ‘make’ and [tu] ‘touch’, which are homophones, would also be produced. The only "contrastive" unit is semantic, which is not what the researcher is necessarily looking for.