The blog Getting Genetics Done features tips for analyzing genomic data, such as this recent post on hierarchical clustering with R using the hclust function. One of the interesting wrinkles with genomic data is that there will generally be many clusters, in which case the traditional tree representation is likely to be an unreadable “fuzzball”:
The post gives some useful tips on how to export the tree data from R and use specialized software to create alternate visualizations, like this circular cladogram:
Getting Genetics Done: Hierarchical Clustering in R
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