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The deunique.tree command reinserts the redundant sequence identiers back into a unique tree. For this tutorial, you should use the files found in the TreeTest.zip archive.
To run the command the names of a tree-file and name-file need to be provided:
mothur > deunique.tree(tree=test.tre, name=test.names)
This will generate a new tree file containing all the sequences: test.deunique.tre.