Recovery of edit paths from inferred protein trees, grouped by size. Five different EEEP settings were used to recover edit paths from 19 672 inferred protein trees with at least one resolved bipartition, via comparison with the inferred MRP supertree. Five types of bar, ordered from left to right, represent 'standard' EEEP runs with no ratchet, a permissive test tree ratchet, a strict test tree ratchet, a permissive reference tree ratchet, and a strict reference tree ratchet. The final, checkered bar for each category represents the total number of cases where at least one type of EEEP run recovered an edit path solution. The total number of protein trees in each size class (e.g., 11–20) is indicated by horizontal lines with a centered open diamond.