| drawtangle | Matching dendrograms |
| finddistance | Clustering strains based on dissimilarity of SNPs |
| maketree | Generating dendrograms for the entire chromosome |
| SampPheno | Loading a sample phenotype data |
| SampSNP | Loading a sample phenotype data |
| snpcor | Correlating SNP dendrograms with the trait dendrogram |
| snpcor.best | Subestting for highest correlations |
| traittree | Clustering strains base on quantitative trait data |
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