Table 1.

Four methods for rooting phylogentic trees

Rooting method	Pros	Cons	Software
Outgroup	Accurate	Must have an outgroup	PAUP
		Long branch attraction	Figtree
			R package: ape (http://www.inside-r.org/packages/cran/ape/docs/unroot)
Midpoint	Fast	Dependent on clocklike data	PAUP
	No outgroup needed	Not good with unbalanced trees	R package: phangorn (https://cran.r-project.org/web/packages/phangorn/phangorn.pdf)
Molecular clock	No outgroup needed	Computationally intense	PAUP
	Robust to violations of the clock		PAML
Bayesian molecular clock	Alternative rootings uncovered	Must customize the prior	Post Root (http://www.stat.osu.edu/~lkubatko/software/phyl_util.html)
	No outgroup needed		Root annotator (http://sourceforge.net/projects/rootannotator/)