Table 1 Summary of ReporTree input types and respective clustering options, with indication of the main outputs provided by this tool
Inputs Metadata and (phylo)genetic data | Clustering options | Main outputs |
|---|---|---|
- Multiple sequence alignment (e.g., core SNP alignment) - SNP/allele matrix (e.g., derived from cg/wgMLST analysis) - List of mutations or VCFs - Pairwise distance matrix (only for HC) | Minimum spanning tree (using GrapeTree) | - Genetic clusters at any (or all) possible distance threshold(s) (partitions table) - Updated metadata table with clustering information (and nomenclature) - Summary reports with the statistics/trends for the derived genetic clusters - Nomenclature history (record of changes in cluster composition and codes between runs) - Summary reports and in-depth cluster analysis for samples of interest - Count/frequency matrices for the derived genetic clusters or for any other indicated grouping variable - Regions of cluster stability - Newick tree (when applicable) |
Hierarchical clustering (using several methods, such as single-linkage) | ||
- Newick tree (e.g., SNP-scaled tree or dendrogram) | Distance between leaves and root or between tree nodes (using TreeCluster) |