Can i use orthofinder for small protein datasets and not full proteome?

Question

[alexandrakortsi]

Hi all,

I have predicted the effector proteins for a range of fungal genomes and i have them in fasta sequences. In order to compare them i need to group them somehow. I thought of using orthofinder but i dont know if its the correct approach or i will introduce any biases. My question is can i use orthofinder grouping (not the phylogenetic tree)? Does anyone has advice on a diferrent way to group them?

[michael.ante]

Do you want to compare them by sequence or by function?

For the later, you can use e.g. InterProScan, KoFamScan.

[alexandrakortsi]

By sequence. Thank you for your response!

Answer 1

[dthorbur]

If you're just using the tool for clustering purposes, I think OrthoFinder might be a little clunky and would recommend using something like mmseqs2 easy-cluster instead. It's fast and one of it's intended purposes. But in theory you could use OrthoFinder just for clustering if you really want to stick to the same tool.