The ordinal quartet method

The utility of ordinal assertions for inferring evolutionary trees from sequence data is examined. If M is a difference matrix derived from a set of sequences then "M(s; x) M(s; y)" is an ordinal assertion supported by M where s, x and y are sequences. Ordinal assertions are shown to be an accurate and robust source of evolutionary information. The following results are presented: A method for inferring quartet topology, the Ordinal Quartet Method, is introduced. Simulations are reported which demonstrate that the Ordinal Quartet Method is significantly more accurate and robust than the popular Weak Four--Point Condition Method. This improvement dramatically increases the accuracy of quartet recombination methods, such as the Short Quartet Method [10] and the Q Method [6] whose accuracy is critically dependent upon the ability to infer quartet topology accurately. It is also demonstrated that, unlike other quartet inference methods such as the Weak Four--Point Condition Method, th...