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TOGA2 is a revised version of Tool to infer Orthologs from Genome Alignments, which doubles down on the strong points of the original tool while reducing memory and runtime requirements and adding multiple new features.
This documentation is aimed to provide you with all the necessary information on how to install, run, and analyse the results of TOGA2. The contents are loosely organised into the following major blocks:
- TOGA2 installation
- Input file preparation
- Description of TOGA2 pipeline, with documented algorithms for different pipeline steps and procedures
- Output file description
- Suggestions on TOGA2 results analysis
A detailed table of contents follows below. You can also look up the contents in the sidebar on the right side of each page.
To facilitate user experience, most of the pages have short introduction sections or information boxes containing the required minimum of knowledge necessary to process the page’s contents. If a certain aspect of the TOGA2 pipeline is better explained elsewhere in this Wiki, the page provides cross-links to respective Wiki sections. If you struggle with the specific terms or their use in the context of TOGA2, consider visiting the Glossary page.
Warning
TOGA2 documentation is currently in progress. Pipeline description and code documentation (e.g., cookbook contents, README, and this Wiki) will be expanded with time.