Complex sentence: Their software is based less strongly on firm mathematical principles than previous methods, but is significantly faster, allowing the fast construction of trees for thousands of species, in comparison to previous methods whose slow performance limited them to only comparing dozens of species at a time.
Split into simpler sentences: Their software is based less strongly on firm mathematical principles than previous methods, but is significantly faster, allowing the fast construction of trees for thousands of species. In comparison, the slow performance of previous methods limited them to only comparing dozens of species at a time.