Roundup is a database of orthologs and their evolutionary distances.

To get started, click retrieve. Alternatively, you can read our documentation here.

Good luck, researchers!

What is Roundup?

Roundup is a large-scale orthology database. The orthologs are computed using the Reciprocal Smallest Distance (RSD) algorithm. This algorithm detects more (and more accurate) orthologs than reciprocal best blast hits and gives each ortholog a score based on its maximum likelihood evolutionary distance.

Every release of Roundup downloads the latest genomes from UniProt and computes orthologs for them. See About for more information about Roundup's data sources and release schedule.

Download a locally-installable version of the RSD algorithm. A tutorial (PDF) about RSD is also available.

We have also run RSD on Amazon Elastic Compute Cloud. The steps and code we used to run RSD on the cloud may be downloaded here.

Database Statistics for Release 4

• Release date: April 15, 2013.
• Number of genomes: 2,044.
• Number of pairs of genomes searched for orthologs using the RSD algorithm: 2,087,946.
• Number of orthologous pairs of genes inferred (for all parameter combinations): 15,276,329,689.

How to Cite

If you use Roundup, please cite Roundup 2.0: Enabling comparative genomics for over 1800 genomes. Deluca TF, Cui J, Jung JY, St Gabriel KC, Wall DP. Bioinformatics. 2012.

If you use the RSD algorithm, please cite Wall, D.P., Fraser, H.B. and Hirsh, A.E. (2003) Detecting putative orthologs, Bioinformatics, 19, 1710-1711.