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I understand that rooted and unrooted phylogenetic trees are similar in structure

But how can they be easily identified as one or the other?

Is it simply based on the presence or lack of a named root (the root is identified as a particular ancestor) or outgroup?

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  • $\begingroup$ At which "stage" do you want to identify the tree? When it's a file (Newick), or when it's a drawn figure? $\endgroup$ – Michael Kuhn Dec 15 '11 at 8:32
  • $\begingroup$ I'd say a drawn figure? Like something you would find on a google search for phylogenetic tree (images.google.com/search?tbm=isch&q=phylogenetic%20tree) $\endgroup$ – arcyqwerty Dec 15 '11 at 8:36
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In case of a drawn figure, either look for the a short stem to the left, or for an explicitly labelled outgroup. Trees derived from phylogenetic analyses are normally unrooted by default, you need to root them by either making an arbitrary (but hopefully informed) decision or by adding an outgroup.

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  • $\begingroup$ So when you say root it by making an arbitrary decision, does that mean labeling a particular ancestral individual as a root? Also, does this consider midpoint rooting? $\endgroup$ – arcyqwerty Dec 15 '11 at 8:43
  • $\begingroup$ Midpoint root is certainly one of the ways you can choose to root your tree. IMHO rooting a tree of species or proteins without an outgroup is done by adding an extra root node. $\endgroup$ – Michael Kuhn Dec 15 '11 at 8:45
  • $\begingroup$ And just to clarify, how would the 'extra root node' appear on a diagram? As just a labeled point from where the rest of the tree branches off from? $\endgroup$ – arcyqwerty Dec 15 '11 at 8:47
  • $\begingroup$ Usually, there's a short stem going in a different direction than all the other leaves. But a labelled point is also fine, I guess $\endgroup$ – Michael Kuhn Dec 15 '11 at 8:51
  • $\begingroup$ Unrooted by default? Which algorithms are you talking about? $\endgroup$ – peri4n Dec 15 '11 at 9:00
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Trees can not be distinguished from each other because every unrooted tree can be made rooted by adding a root and vice versa by deletion.

If you mean dendrograms... the root is always the one node where the distance to each leaf is the same. But I don't know of an unrooted dendrogram.

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  • $\begingroup$ Yes, but how would I be able to tell whether or not a tree has a root Like how to tell between an unrooted tree and a midpoint rooted tree? $\endgroup$ – arcyqwerty Dec 15 '11 at 8:30
  • $\begingroup$ If you really mean trees. They are not distinguishable. $\endgroup$ – peri4n Dec 15 '11 at 8:36

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