Entering edit mode
5.2 years ago
Jess
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0
I want to generate a tree using manhattan distance matrix (normalized to 0-1). This is purely genetic diversity study and no evolutionary changes are involved. I am wondering which is better to use, UPGMA or NJ method? I am assuming that it is okay to use UPGMA since it is not used in inferring evolutionary history (constant molecular clock). However, I have read that "unrooted tree is desired when we do not have a distantly related group (sequence) for comparison or when primary interest is focused only on relationships among the taxa rather than on the directionality of evolutionary change", and the default output of NJ tree is unrooted while UPGMA is necessarily rooted.
Are you sure you really want a phylogeny and not simply a dendrogram from, say, hierarchical clustering?