The new OrthoFinder paper is out now!
In this new work, we introduce major advances in accuracy and scalability, allowing analysis on much larger datasets
www.nature.com/articles/s41...
github.com/OrthoFinder/...
The updated OrthoFinder v3 software boosts accuracy and scalability in phylogenetic orthology inference with massive and diverse datasets.
So is it scalable?
We benchmarked OrthoFinder against other widely used orthology tools
OrthoFinder is the only method able to analyse >1000 species within our time cutoff
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
What else is new?
We now use gene tree–species tree reconciliation to refine orthogroups
This catches cases where distinct orthogroups were mistakenly fused
Most orthology inference tools reply on all-versus-all comparisons between species, which become painfully slow as datasets grow in size. Here, we introduce a new scalable method to circumvent this problem
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
