A logarithm-free subexponential algorithm for minimum quartet inconsistency

Abstract

We give a deterministic algorithm for complete, unweighted minimum quartet inconsistency (MQI) with time and space $2^{O(k^{1/4})}+n^{O(1)}$, where $n$ is the number of taxa and~$k$ is the allowed number of quartet disagreements. This removes the logarithmic factor from the exponent of the MQI bound announced in 2009. The algorithm combines low-error anchoring, chromatic coding, and dynamic programming that accounts for disagreements with all input quartets, with a refined count of colorings and merging states. We also record a generic ETH-based lower bound. The optimality of the fourth-root exponent remains open.