> For the complete documentation index, see [llms.txt](https://cgps.gitbook.io/pathogenwatch/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/trees-clustering-and-context-search/core-genome-tree.md).

# Core Genome Tree

- [About SNP-based trees](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/trees-clustering-and-context-search/core-genome-tree/about-snp-based-trees.md)
- [Core Assignment](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/trees-clustering-and-context-search/core-genome-tree/core-assignment.md)
- [Core Filter](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/trees-clustering-and-context-search/core-genome-tree/core-filter.md)
- [Reference Assignment](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/trees-clustering-and-context-search/core-genome-tree/reference-assignment.md)
- [Tree Construction](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/trees-clustering-and-context-search/core-genome-tree/tree-construction.md)