Using Quartets to Compare the NCD and MCMC Methods for Constructing Phylogenetic Trees

The Normalized Compression Distance (NCD) method, which provides difference matrices from which phylogenetic trees can be constructed, is computationally very fast even on large sets of sequences. The Markov Chain Monte Carlo (MCMC) method, widely used in the literature, is computationally more expensive but is relied on as an accurate method for constructing trees. We look here at results comparing these methods with respect to unrooted quartet trees, which can serve as building blocks for deriving trees on larger sets of sequences.