How can I do UPGMA cluster analysis in Qiime

[sdpapet]

Hi I have some samples from different sites. How want to build a tree (UPGMA cluster) to see the if the samples from similar environment will cluster together.

How can I do it? What kind of distance matrix I can make? (Bray-Curtis). What command I can use to make distance matrix and build the tree?

Thanks,
Ben

[Will Van Treuren]

Hi Ben, 

You will want to use the upgma_cluster.py script in qiime. Any of the distrance metrics available in beta diversity can be used upstream of the upgma_cluster.py script. To build the distance matrix you will want to use 

the script beta_diversity.py.

Hope this helps, 

Will 

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