Pathway Analysis by Randomization Incorporating Structure (PARIS) is a software tool for conducting pathway analysis independent of study design. It is written in C++ and utilizes an SQLite database and variations file (both included in download) for analysis.
From the Bush Lab and the Haines Lab, Mariusz Butkiewicz has developed COCOS, a plugin for the Ensembl Variant Effect Predictor (VEP) plugin for annotating reading frame changes. The plugin captures Amino Acid sequence alterations stemming from variants that produce an altered reading frame, e.g. stop-lost variants and small genetic Insertion and Deletions (InDels). The GitHub repository for COCOS can be found here.