OrthoFinder is not only fast and accurate, it's easy to use
Just provide the complete set of amino acid sequences for your species
If you prefer a specific tree or alignment tool, it's easy to customise
We also provide rich outputs like gene duplications and comparative genomics stats
But is it still accurate?
We benchmarked orthogroups using the OrthoBench dataset
OrthoFinder came out on top
What about ortholog accuracy?
We tested using the gold standard Quest for Orthologs benchmarking service
OrthoFinder scored highly across the board
is there a version of the @official-smbe.bsky.social programme that is just a simple PDF? I struggle with these interactive agenda sites
Get OrthoFinder here github.com/OrthoFinder/...
Read the paper here
www.nature.com/articles/s41...
Our trick: run OrthoFinder on a small subset of species first
Next, we sample representative sequences from each orthogroup to build profiles
Genes from new species are then matched to these profiles to assign them to orthogroups
We avoid the costly all-vs-all step that kills scalability