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OMA Academy

Welcome to the OMA Academy! Here, you will find online exercises which will aid you in becoming more familiar with orthology, phylogenies, and comparative genomics.

Background
OMA (“Orthologous MAtrix”) is a method and database for the inference of orthologs among complete genomes. It can be found at omabrowser.org. Many of the exercises use the OMA browser as a starting point. The OMA pipeline can also run on custom genomic/transcriptomic data using the OMA stand-alone software, and it is even possible to combine precomputed data with custom data by exporting parts of the OMA database.


Tables of contents
  1. Exploring Orthology with the OMA Browser
  2. OMAmer
  3. FastOMA
  4. Estimating a Species Tree
  5. BGA OMA and OMArk for homology exploration and gene annotation quality control

Learning objectives

  • Navigate and use the OMA browser to extract different types of homology information and to infer evolutionary events such as duplications, gains, and losses in a particular gene family.
  • Install and run FastOMA, a software to infer orthology on your own genomes.
  • Build and evaluate gene trees and (optional) species trees.

    • Useful materials

    When undertaking these exercises, the following materials may be useful:

  • OMA Help pages: Orthology Basics, Types of homologs, Access the OMA Data, Catalog of Tools, and Glossary
  • OMA Standalone documentation
  • OMA Primer
  • F1000 phylogenetics tree paper
  • OMA Standalone blog post

    • For Modules 2-4, it is best to use the GitPod workspace available here.

    You will find the following buttons to interact with the exercises:


    Asking questions

    We remain available to answer your questions after this course. Please direct your emails to contact@omabrowser.org with a subject starting with "OMA Academy".

    However, for some general questions about OMA, we often receive requests through BioStars. Please consider asking your question there, including the tags "OMA" and "orthologs". We monitor BioStars for such questions and will answer them directly on that platform.