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?
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.