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I have whole genome aligned sequences of four beetle populations of same species. I wish to construct a phylogenetic tree with the four. However, I am unable to find a suitable outgroup of the species, so I cannot use an outgroup to root the tree. Is there a particular method that one can use to construct a tree without an outgroup? I found that the MEGA software does this well. What is the theory and understanding of constructing a tree without an outgroup? what are the implications of constructing a tree without an outgroup? Ar the distances between trees measured relative to one another?

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marked as duplicate by Remi.b, AliceD, James, WYSIWYG Dec 1 '16 at 7:05

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    $\begingroup$ Isn't a phylogenetic tree without an outgroup just an unrooted tree? $\endgroup$ – Luigi Nov 30 '16 at 13:46
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    $\begingroup$ Related. $\endgroup$ – Luigi Nov 30 '16 at 13:47
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Most classic phylogeny reconstruction algorithms root the tree a posteriori, based on the outgroup chosen by the user. The tree is actually inferred and internally represented without root.

Therefore, if you use a program that asks you an outgroup, it is likely that you can just choose an arbitrary one and later "de-root" the obtained tree.

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