I can't answer the question about file formats, but it should be possible to
analyze the cell cycle distributions that have a large group of early S phase
cells with Multicycle. Peter Rabinovitch incorporated an additional S phase
peak option, which came from a model I published in Cytometry 1:71-77 (1980),
and it does a good job of analyzing unusual S phase distributions. I
originally developed it to analyze synchronous populations.
Mike Fox