Dear Olivier,

HyPhy buffers all console output and does it one line at a time and there is no fflush equivalent. I've been thinking about adding a progress bar functionality to HyPhy via a built-in call which can pop up windows in GUI versions, and perhaps a console [...] or spinning pipes or something like that.

Shouldn't be too hard to do. I'll keep you posted.

Cheers,
Sergei