jaredbernard

@ShadoWyyyy, I think you're right; the input for cafe_fig is supposed to be a `.cafe` file type, and CAFE5 seems to have done away with this. @benfulton, do you know...

I think we are all interested in something similar to what Kremer shows in [CAFE_fig](https://github.com/LKremer/CAFE_fig), but it requires the `.cafe` file type.

Some have used it for this purpose, for example [Hazzouri et al. 2020](https://doi.org/10.1038/s42003-020-1060-8).

Thanks for getting back to me, @benfulton. I adjusted the syntax, but still not getting anything. The only output is a list of `.fa` files in the directory, but no...

Related to this topic, I noticed that in the tutorial.md under "Summarizing the Output" it says "If you open file results/base_clade_results.txt, you will see, for each branch, how many families...