Get OrthoFinder here github.com/OrthoFinder/...

Read the preprint here www.biorxiv.org/content/10.1...

Millions of species here we come!

(10/10)

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 (9/10)

What else is new?

We now use gene tree–species tree reconciliation to refine orthogroups

This catches cases where distinct orthogroups were mistakenly fused (8/10)

What about ortholog accuracy?

We tested using the gold standard Quest for Orthologs benchmarking service

OrthoFinder scored highly across the board (7/10)

But is it still accurate?

We benchmarked orthogroups using the OrthoBench dataset

OrthoFinder came out on top (6/10)

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 (5/10)

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 (4/10)

Most tools rely on all-versus-all comparisons between species

This becomes painfully slow as datasets grow

We needed a better way (3/10)

Millions of species are being sequenced

That’s a huge opportunity, but also a major challenge
How can we ramp up scalability without compromising accuracy?

That’s exactly what we set out to solve in this update (2/10)

I'll do the top row!

Buff tip, peach blossom, brimstone!