Much of the information here is also contained in the documentation of the Python modules themselves. A full list of command-line parameters can be printed to screen using the help option, with short descriptions for each one:
python program.py help
python program.py -help
python program.py -hDetails of command-line options specific to each program can also be found in the distributed readme.txt and readme.html files.
If stuck, or something is unclear, then please e-mail me (seqsuite@gmail.com) whatever question you have. If it is the results of an error message, then please send me that and the log file too.
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