Far more interesting than the software is the chapter in the CIA book Psychology of Intelligence Analysis where they describe the method:

Analysis of competing hypotheses, sometimes abbreviated ACH, is a tool to aid judgment on important issues requiring careful weighing of alternative explanations or conclusions. It helps an analyst overcome, or at least minimize, some of the cognitive limitations that make prescient intelligence analysis so difficult to achieve.

ACH is an eight-step procedure grounded in basic insights from cognitive psychology, decision analysis, and the scientific method. It is a surprisingly effective, proven process that helps analysts avoid common analytic pitfalls. Because of its thoroughness, it is particularly appropriate for controversial issues when analysts want to leave an audit trail to show what they considered and how they arrived at their judgment.

Summary and conclusions:

Three key elements distinguish analysis of competing hypotheses from conventional intuitive analysis.

• Analysis starts with a full set of alternative possibilities, rather than with a most likely alternative for which the analyst seeks confirmation. This ensures that alternative hypotheses receive equal treatment and a fair shake.
• Analysis identifies and emphasizes the few items of evidence or assumptions that have the greatest diagnostic value in judging the relative likelihood of the alternative hypotheses. In conventional intuitive analysis, the fact that key evidence may also be consistent with alternative hypotheses is rarely considered explicitly and often ignored.
• Analysis of competing hypotheses involves seeking evidence to refute hypotheses. The most probable hypothesis is usually the one with the least evidence against it, not the one with the most evidence for it. Conventional analysis generally entails looking for evidence to confirm a favored hypothesis.