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Welcome to the TOGA wiki!

TOGA is a new method that integrates gene annotation, inferring orthologs and classifying genes as intact or lost.

TOGA implements a novel machine learning based paradigm to infer orthologous genes between related species and to accurately distinguish orthologs from paralogs or processed pseudogenes.

This tutorial explains how to get started using TOGA. It shows how to install and execute TOGA, and how to handle possible issues that may occur.

TO BE FILLED

Detailed documentation

• Installation and configuration
• Usage and best practices
• Creating Custom XGBoost Models for TOGA
• Interpreting results
• Troubleshooting
• FAQ
• Contributing

Citing

Kirilenko BM, Munegowda C, Osipova E, Jebb D, Sharma V, Blumer M, Morales AE, Ahmed AW, Kontopoulos DG, Hilgers L, Lindblad-Toh K, Karlsson EK, Zoonomia Consortium, Hiller M. Integrating gene annotation with orthology inference at scale. Science, 380(6643), eabn3107, 2023