What is the difference between Roary and Orthofinder

Question

[Juliana]

Hi, I would like to know the difference between these two tools. Both tools create family genes through a comparison of genomes.

I would like to infer the unique genes that are in a genome by doing a comparison between two genomes but I do not which tool should I use.

Thanks.

[Joe]

They both do the same thing more or less. I haven't used Orthofinder but Roary is very user friendly. If you don't have a specific reason to choose Orthofinder Roary should serve you well.

[Dunois]

OrthoFinder is also pretty user-friendly. I think the main difference would boil down to the input formats. Roary uses gff3 flat files I think, while OrthoFinder needs protein sequence FASTA files.

It'd probably be a bad idea to run OrthoFinder on just two input data sets: https://davidemms.github.io/orthofinder_tutorials/orthofinder-best-practices.html (I assume this is what the OP wants to do). I guess the tool wouldn't be able to take full advantage of its gene tree-building capabilities, and it essentially ends up performing an RBH (reciprocal best hit) search. Might as well just use blast or MMseqs2 easy-rbh or DIAMOND in that case, and filter out the RBH hits from the data set of interest to recover the "unique" genes.

Can't really comment on Roary since I've never used it before.