Table 1.

The various executables included in the TomoMiner software package.

Parallel processing programs	Description
tm_server	Run a server
tm_worker	Run a worker which will process subproblems
tm_watch	Report progress and statistics on the server
Utility programs	Description
tm_align	Calculate optimal alignment between two subtomograms using fast rotational matching
tm_fsc	Calculate the Fourier Shell Correlation(FSC) between two aligned structures
tm_corr	Calculate the correlation score of the best alignment between two subtomograms
Analysis programs	Description
tm_classify	Reference-free or reference-based subtomogram classification
tm_average	Reference-free or reference-based subtomogram alignment and global averaging
tm_match	Template matching