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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. OMA (“Orthologous MAtrix”) is a method and database for the inference of orthologs among complete genomes. It can be found at omabrowser.org.

Tables of contents
  1. Exploring Orthology with the OMA Browser
  2. OMA Standalone
  3. Gene Trees
  4. Estimating a Species Tree
  5. Automated Queries
  6. Synteny

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 OMA standalone, a piece of software to infer orthology on your own genomes.
  • Build and evaluate gene trees and (optional) species trees.
  • (Optional) Automate querying of orthology data.
  • 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
  • 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.