Tutorials
These tutorials take you from getting the input files to interpreting the results of OrthoFinder. If you are new to OrthoFinder, read them in this order.
- Getting Input Data shows how to download the proteomes of your species from Ensembl, NCBI or Phytozome, and keep one transcript per gene.
- Beginner Tutorial shows how to install OrthoFinder, run it on the example data, and explore its results.
- Guide to Results describes what each results file contains.
Understanding Orthology explains orthologs, paralogs and orthogroups, and why OrthoFinder works with orthogroups. For more than about 100 species, or to add species to an earlier analysis, see the Advanced Tutorial. For the options to stop and restart an analysis, run the sequence searches yourself, or choose other programs, see Advanced Usage.
📄 All the tutorials in one document, for the latest release, are in OrthoFinder3_tutorial.pdf
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1. Advanced Tutorial
1 minute read |
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2. Advanced Usage
1 minute read |
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3. Getting Input Data
5 minute read |
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4. Guide to Results
6 minute read |
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5. Understanding Orthology
4 minute read |
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6. Beginner Tutorial
10 minute read |