About The OMA collection

Orthologs are genes in different species that originated from the same gene in their last common ancestral genome, and are a cornerstone for comparative genomics, phylogenetics, and for the prediction of function in newly annotated genomes. With the high number of genomes sequenced in recent decades, computational orthology inference has become commonplace. One such inference method is Orthologous Matrix, or OMA¹. The OMA Browser (https://omabrowser.org) is a database that provides orthology information among more than 2300 genomes across the tree of life.  Additionally, the OMA algorithm is freely available as an open source software tool². Many analyses are possible with the OMA, including:

• Identifying all homologsーincluding orthologs, paralogs, and homoeologsーof a gene or genes in a given set of organisms.

• Obtaining, visualizing, and using Hierarchical Orthologous Groups, or nested gene families which all originated from a single ancestral gene.

• Tracing the evolutionary history of gene families, including duplications, gains, and losses.

• Assessing the conservation of local genomic neighbourhoods across multiple species.

• Applying the OMA pipeline to custom genome/transcriptome data.

• Propagating functional annotations between specific genomes.

• Identifying orthologous marker genes to infer a phylogenetic species tree.

In this collection, we provide tutorials and protocols on how to leverage the tools provided by OMA to analyse your data. We also welcome any biological applications, commentaries, conference posters/slides, or any other published work that uses OMA. 

1. Altenhoff, A. M. et al. The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces. Nucleic Acids Res. 46, D477–D485 (2018).

2. Altenhoff, A. M. et al. OMA standalone: orthology inference among public and custom genomes and transcriptomes. Genome Res. 29, 1152–1163 (2019).