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wrote...
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2 months ago
Hi!
I was wondering if anyone out there would know why I should go with an UPGMA guide tree based method as opposed to a neighborjoining (NJ) guide tree based method.
From what I can tell, UPGMA creates rooted trees and NJ creates unrooted trees. But why would I choose one over the other?
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wrote...
2 months ago
They use different algorithms to build the from a distance matrix. You can check the details of those algorithms for the Wikipedia:

http://en.wikipedia.org/wiki/UPGMA
http://en.wikipedia.org/wiki/Neighbor_joining

The most important practical issues: UPGMA provides rooted tree as a result, while NJ unrooted, and you have to take care proper rooting the NJ tree afterward.

Also, UPGMA is regarded as an unreliable method, so I would prefer to use NJ.

Bootstrapping is a re-sampling method used in phylogenetics to estimate the reliability of individual branching points of a tree:

http://en.wikipedia.org/wiki/Bootstrapping_(statistics)

As a first approach, bootstrap values tell you how much you can "trust" a branch on a phylogenetic tree. The bigger the better. Values over 0.9 (90%) are usually OK. (But that depends on your data and research question too.) Values below 0.6 (60%) are usually no-go.
Source Online
wrote...
2 months ago
The Unweighted Pair-Group Method  with Arithmetic Averaging (UPGMA) algorithm (left) assumes equal rates of evolution, so that branch tips come out equal. The Neighbor-Joining (NJ) (right) algorithm allows for unequal rates of evolution, so that branch lengths are proportional to amount of change. If rates on different branches are not markedly unequal, the branching orders produced by the two methods will not differ, as in this example with Carnivora.



Alternative UPGMA & NJ phenetic analyses of Panda relationships
wrote...
2 months ago
Thanks guys!
One further question - why would a rooted or unrooted tree or assuming equal or unequal rates of evolution be beneficial for one scenario versus another?
wrote...
Educator
2 months ago


The first sentence explains the benefit of one over the other
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wrote...
2 months ago
Thank you very much for your help! Appreciate all the insight. Makes perfect sense when someone explains it like that.
wrote...
Educator
2 months ago
Our pleasure Smiling Face with Open Mouth

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