The Short Quartet Method

Reconstructing phylogenetic (evolutionary) trees is a major research problem in biology, but unfortunately the current methods are either inconsistent somewhere in the parameter space (and hence do not reconstruct the tree even given unboundedly long sequences), have poor statistical power (and hence require extremely long sequences on large or highly divergent trees), or have computational requirements that are excessive. We describe in this paper a new method, which we call the Short Quartet Method, for inferring evolutionary trees. The Short Quartet Method has great statistical power, is provably consistent throughout the parameter space, and uses only polynomial time. We present the results of experimental studies based upon simulations of sequence evolution that demonstrate its greater statistical power than neighbor-joining 33], perhaps the most popular method for phylogenetic tree inference among molecular biologists.

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