9e0dc6c5_BAMBE_manual_Run_control_file_options__Description
[Option] initial-pia [Choices] Comma separated list of positive numbers between 0 and 1. Default is 0.25 if estimate-pi is false. [Description] 
The initial stationary probability of the base A. There must be a value specified for each site-category used if estimate-pi is false.
BAMBE manual
Description