STRIDE is a method for inferring the root of a species tree by analysing the distribution of gene duplication events in the genomes of the species in the tree.

Its fast and easy to use. It is also the method used by OrthoFinder to infer the root of the species tree it computes from all-vs-all proteome comparisons.

You can download and install STRIDE here

If you use stride in your work please cite:

Emms DM and Kelly S (2017). STRIDE: Species Tree Root Inference From Gene Duplication Events. Molecular Biology and Evolution 34(12): 3267-3278