PBjam can be roughly divided into two parts, the mode ID and the peakbagging stages. PBjam currently supports mode ID with the asy_peakbag module, and peakbagging with the peakbag module. Additional methods for these steps may be added to PBjam in the future.

The session and star modules are wrappers for many of the methods in asy_peakbag and peakbag, to help set up the analysis of one or more stars in a pipeline-like fashion.