I want to use something/anything to calculate changes in gene family sizes in a way that accounts for phylogenetic history. My tree has some 100 land plants and some 20k homologous groups.
Issue: I previously used CAFE5 for this purpose but turns out my current dataset is too big for CAFE5. I consulted the authors of CAFE5 about this here : https://groups.google.com/g/hahnlabcafe/c/Vgp4Ry1m1l0 and it does seem to be the case that my tree might be a bit too large for CAFE5.
So, I am trying to see if people can suggest something like a drop-in replacement for CAFE5 for larger workloads or perhaps let me know about some of the approaches they took to handling gigantic datasets to generate estimations for gene family size changes. I am currently going though papers that have cited CAFE to see if I can find anything but that is more or less like looking for a needle in a haystack. Any suggestions for a situation like this?
The newick I am working on is linked here: https://drive.google.com/file/d/1v-dayYkQEX7rCRuXL7Kj_HV8ckcsPeRD/view?usp=sharing