> 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/lineage-and-genotyping.md).

# Lineage Assignment & Genotyping Methods

- [cgMLST](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/lineage-and-genotyping/cgmlst.md)
- [Genotyphi](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/lineage-and-genotyping/genotyphi.md)
- [Geno7PET](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/lineage-and-genotyping/geno7pet.md): Sublineage assignments for Vibrio cholerae 7PET pandemic strains
- [HierCC](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/lineage-and-genotyping/finding-hiercc-codes-with-hclink.md): Linking Enterobase HierCC clusters using the hclink software
- [Kleborate](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/lineage-and-genotyping/kleborate.md): Klebsiella comprehensive AMR and typing analysis software.
- [Klebsiella LIN Codes](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/lineage-and-genotyping/klebsiella-lin-codes.md): The Pathogenwatch LIN code tool infers Klebsiella lineage codes based on references from the Pasteur/PubMLST resource.
- [MLST](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/lineage-and-genotyping/mlst.md)
- [NG-MAST](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/lineage-and-genotyping/ng-mast.md)
- [NG-STAR](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/lineage-and-genotyping/ng-star.md): Resistance-based typing of Neisseria gonorrhoeae
- [Pangolin](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/lineage-and-genotyping/pangolin.md): SARS-CoV-2 lineage assignment tool
- [PopPUNK](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/lineage-and-genotyping/poppunk.md): S. pneumoniae GPSC strain assignment
- [SARS-CoV-2 Notable Mutations](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/lineage-and-genotyping/sars-cov-2-notable-mutations.md): Identification of mutations described in the Type Variants database
- [Vista](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/lineage-and-genotyping/vista.md): Virulence and genotype annotation tool for Vibio cholerae