Flow charts can be an excelent way to document our understanding of a program. No utility can possibly do this for us. Use any tool(s) that you find useful.
I suggest perltidy as a substitute for a flow chart program only in the sense that both are intended to reveal the structure of the code. I find it easier to grasp that structure from systematically indented code rather than from machine generated charts which spread the same information over several times as many pages. Again, my advice is use what works for you!