11 June 2016 4 8K Report

Hello, 

suppose I have constructed a phylogenetic tree with all OTU sequences and reference sequences. I now want to have a tree containing only the OTU sequences. Is it a good practical to remove the reference sequences from the original tree? Will such handling interfere the topology/clustering of the OTU sequences. 

I read somewhere in web stating "Deleting nodes from phylogenies is risky business! Deleting nodes is unlikely to give you the same phylogeny as re-running the tree with the corresponding sequences removed." how will node deleting interfere with the clustering alone? Are there relevant literatures on this matter?

Thank you in advance and best regards

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