Gregg Thomas

Hi Haley, Thanks for the info, its very useful. I went ahead and tried an lmerge as the last step instead of prune, but I can't seem to get it...

I'm not sure about that code snippet, but I think using single-copy groups (one gene in all species) in these analyses is necessary. These groups are still informative when estimating...

I'm not sure about category 2. I think that should be families with *1 or more* gene copies in *more than one clade*. But I'm not sure about it in...

Hi, I'm not sure I have a solution for you right off the bat, but I just wanted to note that an error rate of 0.8125 is extremely high. That...

I don't think either command lets the user know which families are being filtered. I don't use the `max_size` command, but I agree that it would be a nice feature...

Hi, Did you download the report analysis script from this page? https://iu.app.box.com/v/cafetutorial-files/folder/22161236877 If so, you must also download the cafecore.py file and place it in the same directory as the...

Hi, I think this is happening because the report_analysis script unfortunately can't handle node labels on the tree. All of your internal nodes seem to have the label '1' (except...

Hi all, Sorry I missed this post. This is likely because your input tree has internal node labels, which CAFE can handle but the report analysis script cannot. This is...

There used to be a `report_analysis.py` script, but I'm not sure it is supported any more since development has moved on to [CAFE5](https://github.com/hahnlab/CAFE5). Maybe @benfulton could provide more info about...